diff --git a/Marlin/src/HAL/HAL_DUE/DebugMonitor_Due.cpp b/Marlin/src/HAL/HAL_DUE/DebugMonitor_Due.cpp
new file mode 100644
index 0000000000..b7130a45cb
--- /dev/null
+++ b/Marlin/src/HAL/HAL_DUE/DebugMonitor_Due.cpp
@@ -0,0 +1,238 @@
+/**
+ * Marlin 3D Printer Firmware
+ * Copyright (C) 2016 MarlinFirmware [https://github.com/MarlinFirmware/Marlin]
+ *
+ * Based on Sprinter and grbl.
+ * Copyright (C) 2011 Camiel Gubbels / Erik van der Zalm
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef ARDUINO_ARCH_SAM
+
+#include "../../inc/MarlinConfig.h"
+#include "../../Marlin.h"
+
+// Debug monitor that dumps to the Programming port all status when
+// an exception or WDT timeout happens - And then resets the board
+
+// All the Monitor routines must run with interrupts disabled and
+// under an ISR execution context. That is why we cannot reuse the
+// Serial interrupt routines or any C runtime, as we don't know the
+// state we are when running them
+
+// A SW memory barrier, to ensure GCC does not overoptimize loops
+#define sw_barrier() asm volatile("": : :"memory");
+
+// (re)initialize UART0 as a monitor output to 250000,n,8,1
+static void TXBegin(void) {
+
+  // Disable UART interrupt in NVIC
+  NVIC_DisableIRQ( UART_IRQn );
+
+  // Disable clock
+  pmc_disable_periph_clk( ID_UART );
+
+  // Configure PMC
+  pmc_enable_periph_clk( ID_UART );
+
+  // Disable PDC channel
+  UART->UART_PTCR = UART_PTCR_RXTDIS | UART_PTCR_TXTDIS;
+
+  // Reset and disable receiver and transmitter
+  UART->UART_CR = UART_CR_RSTRX | UART_CR_RSTTX | UART_CR_RXDIS | UART_CR_TXDIS;
+
+  // Configure mode: 8bit, No parity, 1 bit stop
+  UART->UART_MR = UART_MR_CHMODE_NORMAL | US_MR_CHRL_8_BIT | US_MR_NBSTOP_1_BIT | UART_MR_PAR_NO;
+
+  // Configure baudrate (asynchronous, no oversampling) to 250000 bauds
+  UART->UART_BRGR = (SystemCoreClock / (250000 << 4));
+
+  // Enable receiver and transmitter
+  UART->UART_CR = UART_CR_RXEN | UART_CR_TXEN;
+}
+
+
+// Send character through UART with no interrupts
+static void TX(char c) {
+  while (!(UART->UART_SR & UART_SR_TXRDY)) { WDT_Restart(WDT); sw_barrier(); };
+  UART->UART_THR = c;
+}
+
+// Send String through UART
+static void TX(const char* s) {
+  while (*s) {
+    TX(*s++);
+  }
+}
+
+static void TXDigit(uint32_t d) {
+  if (d < 10) TX((char)(d+'0'));
+  else if (d < 16) TX((char)(d+'A'-10));
+  else TX('?');
+}
+
+// Send Hex number thru UART
+static void TXHex(uint32_t v) {
+  TX("0x");
+  for (int i=0; i<8; i++, v <<= 4) {
+    TXDigit((v >> 28) & 0xF);
+  }
+}
+
+/**
+ * HardFaultHandler_C:
+ * This is called from the HardFault_HandlerAsm with a pointer the Fault stack
+ * as the parameter. We can then read the values from the stack and place them
+ * into local variables for ease of reading.
+ * We then read the various Fault Status and Address Registers to help decode
+ * cause of the fault.
+ * The function ends with a BKPT instruction to force control back into the debugger
+ */
+extern "C"
+void HardFault_HandlerC(unsigned long *hardfault_args, unsigned long cause) {
+
+  static const char* causestr[] = {
+    "NMI","Hard","Mem","Bus","Usage","Debug","WDT","RSTC"
+  };
+
+  // Dump report to the Programming port (interrupts are DISABLED)
+  TXBegin();
+  TX("\n\n## Software Fault detected ##\n");
+  TX("Cause: "); TX(causestr[cause]); TX('\n');
+  TX("R0   : "); TXHex(((unsigned long)hardfault_args[0])); TX('\n');
+  TX("R1   : "); TXHex(((unsigned long)hardfault_args[1])); TX('\n');
+  TX("R2   : "); TXHex(((unsigned long)hardfault_args[2])); TX('\n');
+  TX("R3   : "); TXHex(((unsigned long)hardfault_args[3])); TX('\n');
+  TX("R12  : "); TXHex(((unsigned long)hardfault_args[4])); TX('\n');
+  TX("LR   : "); TXHex(((unsigned long)hardfault_args[5])); TX('\n');
+  TX("PC   : "); TXHex(((unsigned long)hardfault_args[6])); TX('\n');
+  TX("PSR  : "); TXHex(((unsigned long)hardfault_args[7])); TX('\n');
+
+  // Configurable Fault Status Register
+  // Consists of MMSR, BFSR and UFSR
+  TX("CFSR : "); TXHex((*((volatile unsigned long *)(0xE000ED28)))); TX('\n');
+
+  // Hard Fault Status Register
+  TX("HFSR : "); TXHex((*((volatile unsigned long *)(0xE000ED2C)))); TX('\n');
+
+  // Debug Fault Status Register
+  TX("DFSR : "); TXHex((*((volatile unsigned long *)(0xE000ED30)))); TX('\n');
+
+  // Auxiliary Fault Status Register
+  TX("AFSR : "); TXHex((*((volatile unsigned long *)(0xE000ED3C)))); TX('\n');
+
+  // Read the Fault Address Registers. These may not contain valid values.
+  // Check BFARVALID/MMARVALID to see if they are valid values
+  // MemManage Fault Address Register
+  TX("MMAR : "); TXHex((*((volatile unsigned long *)(0xE000ED34)))); TX('\n');
+
+  // Bus Fault Address Register
+  TX("BFAR : "); TXHex((*((volatile unsigned long *)(0xE000ED38)))); TX('\n');
+
+  // Reset controller
+  NVIC_SystemReset();
+  while(1) { WDT_Restart(WDT); }
+}
+
+__attribute__((naked)) void NMI_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#0             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void HardFault_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#1             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void MemManage_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#2             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void BusFault_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#3             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void UsageFault_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#4             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void DebugMon_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#5             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void WDT_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#6             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+__attribute__((naked)) void RSTC_Handler(void) {
+  __asm volatile (
+    " tst lr, #4            \n"
+    " ite eq                \n"
+    " mrseq r0, msp         \n"
+    " mrsne r0, psp         \n"
+    " mov r1,#7             \n"
+    " b HardFault_HandlerC  \n"
+  );
+}
+
+#endif
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_Due.cpp b/Marlin/src/HAL/HAL_DUE/HAL_Due.cpp
index 17abbff991..44fd6a019f 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_Due.cpp
+++ b/Marlin/src/HAL/HAL_DUE/HAL_Due.cpp
@@ -34,6 +34,7 @@
 #include "../HAL.h"
 
 #include <Wire.h>
+#include "usb/usb_task.h"
 
 // --------------------------------------------------------------------------
 // Externals
@@ -73,6 +74,18 @@ uint16_t HAL_adc_result;
 // Public functions
 // --------------------------------------------------------------------------
 
+// HAL initialization task
+void HAL_init(void) {
+  // Initialize the USB stack
+  usb_task_init();
+}
+
+// HAL idle task
+void HAL_idletask(void) {
+  // Perform USB stack housekeeping
+  usb_task_idle();
+}
+
 // disable interrupts
 void cli(void) { noInterrupts(); }
 
@@ -82,14 +95,13 @@ void sei(void) { interrupts(); }
 void HAL_clear_reset_source(void) { }
 
 uint8_t HAL_get_reset_source(void) {
-  switch ((RSTC->RSTC_SR >> 8) & 7) {
-    case 0: return RST_POWER_ON; break;
-    case 1: return RST_BACKUP; break;
-    case 2: return RST_WATCHDOG; break;
-    case 3: return RST_SOFTWARE; break;
-    case 4: return RST_EXTERNAL; break;
-    default:
-      return 0;
+  switch ((RSTC->RSTC_SR >> 8) & 0x07) {
+    case 0: return RST_POWER_ON;
+    case 1: return RST_BACKUP;
+    case 2: return RST_WATCHDOG;
+    case 3: return RST_SOFTWARE;
+    case 4: return RST_EXTERNAL;
+    default: return 0;
   }
 }
 
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_Due.h b/Marlin/src/HAL/HAL_DUE/HAL_Due.h
index f3c50927f2..4f574ecbd2 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_Due.h
+++ b/Marlin/src/HAL/HAL_DUE/HAL_Due.h
@@ -160,14 +160,15 @@ void toneInit();
 void tone(const pin_t _pin, const unsigned int frequency, const unsigned long duration=0);
 void noTone(const pin_t _pin);
 
-// Enable hooks into idle and setup for USB stack
+// Enable hooks into idle and setup for HAL
 #define HAL_IDLETASK 1
 #define HAL_INIT 1
+void HAL_idletask(void);
+void HAL_init(void);
+
 #ifdef __cplusplus
   extern "C" {
 #endif
-void HAL_idletask(void);
-void HAL_init(void);
 char *dtostrf (double __val, signed char __width, unsigned char __prec, char *__s);
 #ifdef __cplusplus
   }
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
index 06b6d25b89..131318c159 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
+++ b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
@@ -96,6 +96,15 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency) {
   IRQn_Type irq = TimerConfig[timer_num].IRQ_Id;
   uint32_t channel = TimerConfig[timer_num].channel;
 
+  // Disable interrupt, just in case it was already enabled
+  NVIC_DisableIRQ(irq);
+
+  // Disable timer interrupt
+  tc->TC_CHANNEL[channel].TC_IDR = TC_IDR_CPCS;
+
+  // Stop timer, just in case, to be able to reconfigure it
+  TC_Stop(tc, channel);
+
   pmc_set_writeprotect(false);
   pmc_enable_periph_clk((uint32_t)irq);
   NVIC_SetPriority(irq, TimerConfig [timer_num].priority);
@@ -103,12 +112,16 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency) {
   // wave mode, reset counter on match with RC,
   TC_Configure(tc, channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP_RC | TC_CMR_TCCLKS_TIMER_CLOCK1);
 
+  // Set compare value
   TC_SetRC(tc, channel, VARIANT_MCK / 2 / frequency);
+
+  // And start timer
   TC_Start(tc, channel);
 
   // enable interrupt on RC compare
   tc->TC_CHANNEL[channel].TC_IER = TC_IER_CPCS;
 
+  // Finally, enable IRQ
   NVIC_EnableIRQ(irq);
 }
 
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
index 0429746e6b..2fbe4480fe 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
+++ b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
@@ -109,23 +109,12 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
   return pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_CV;
 }
 
-FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const hal_timer_t counter) {
-  const tTimerConfig * const pConfig = &TimerConfig[timer_num];
-  pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_CV = counter;
-}
-
 // if counter too high then bump up compare
 FORCE_INLINE static void HAL_timer_restrain(const uint8_t timer_num, const uint16_t interval_ticks) {
   const hal_timer_t mincmp = HAL_timer_get_count(timer_num) + interval_ticks;
   if (HAL_timer_get_compare(timer_num) < mincmp) HAL_timer_set_compare(timer_num, mincmp);
 }
 
-// if counter too high then clear it
-FORCE_INLINE static void HAL_timer_restrain_count(const uint8_t timer_num, const uint16_t interval_ticks) {
-  const hal_timer_t mincmp = HAL_timer_get_count(timer_num) + interval_ticks;
-  if (HAL_timer_get_compare(timer_num) < mincmp) HAL_timer_set_count(timer_num, 0);
-}
-
 void HAL_timer_enable_interrupt(const uint8_t timer_num);
 void HAL_timer_disable_interrupt(const uint8_t timer_num);
 bool HAL_timer_interrupt_enabled(const uint8_t timer_num);
diff --git a/Marlin/src/HAL/HAL_DUE/Tone.cpp b/Marlin/src/HAL/HAL_DUE/Tone.cpp
index 1b8a3122b7..c097e1e4ca 100644
--- a/Marlin/src/HAL/HAL_DUE/Tone.cpp
+++ b/Marlin/src/HAL/HAL_DUE/Tone.cpp
@@ -33,17 +33,10 @@
 static pin_t tone_pin;
 volatile static int32_t toggles;
 
-void toneInit() {
-  HAL_timer_start(TONE_TIMER_NUM, 100000);
-  HAL_timer_disable_interrupt(TONE_TIMER_NUM);
-}
-
 void tone(const pin_t _pin, const unsigned int frequency, const unsigned long duration) {
   tone_pin = _pin;
   toggles = 2 * frequency * duration / 1000;
-  HAL_timer_set_count(TONE_TIMER_NUM, 0);  // ensure first beep is correct (make sure counter is less than the compare value)
-  HAL_timer_set_compare(TONE_TIMER_NUM, VARIANT_MCK / 2 / 2 / frequency); // 84MHz / 2 prescaler / 2 interrupts per cycle /Hz
-  HAL_timer_enable_interrupt(TONE_TIMER_NUM);
+  HAL_timer_start(TONE_TIMER_NUM, 2 * frequency);
 }
 
 void noTone(const pin_t _pin) {
@@ -60,7 +53,6 @@ HAL_TONE_TIMER_ISR {
     digitalWrite(tone_pin, (pin_state ^= 1));
   }
   else noTone(tone_pin);                         // turn off interrupt
-  HAL_timer_restrain_count(TONE_TIMER_NUM, 10);  // make sure next ISR isn't delayed by up to 2 minutes
 }
 
 #endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/ctrl_access.c b/Marlin/src/HAL/HAL_DUE/usb/ctrl_access.c
index a57c54fee6..0ec14e0b8f 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/ctrl_access.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/ctrl_access.c
@@ -642,5 +642,6 @@ U16 stream_stop(U8 id)
 
 //! @}
 
-#endif  // ACCESS_STREAM == true
-#endif
\ No newline at end of file
+#endif // ACCESS_STREAM
+
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/sysclk.c b/Marlin/src/HAL/HAL_DUE/usb/sysclk.c
index 2328a0853f..899244dd88 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/sysclk.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/sysclk.c
@@ -119,4 +119,4 @@ void sysclk_disable_usb(void)
 /**INDENT-ON**/
 /// @endcond
 
-#endif
\ No newline at end of file
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/udc.c b/Marlin/src/HAL/HAL_DUE/usb/udc.c
index 6995d20b56..a4521be832 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/udc.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/udc.c
@@ -1146,4 +1146,4 @@ bool udc_process_setup(void)
 
 //! @}
 
-#endif
\ No newline at end of file
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/udi_cdc.c b/Marlin/src/HAL/HAL_DUE/usb/udi_cdc.c
index c8ab19b4b3..e54ee570fa 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/udi_cdc.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/udi_cdc.c
@@ -1152,4 +1152,4 @@ iram_size_t udi_cdc_write_buf(const void* buf, iram_size_t size)
 
 //@}
 
-#endif
\ No newline at end of file
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/udi_cdc_desc.c b/Marlin/src/HAL/HAL_DUE/usb/udi_cdc_desc.c
index 98e8ba194d..8f730ba823 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/udi_cdc_desc.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/udi_cdc_desc.c
@@ -255,5 +255,7 @@ UDC_DESC_STORAGE udc_config_t udc_config = {
 
 //@}
 //@}
-#endif
-#endif
+
+#endif // SDSUPPORT
+
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/udi_composite_desc.c b/Marlin/src/HAL/HAL_DUE/usb/udi_composite_desc.c
index d4b155e014..3c5f001a26 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/udi_composite_desc.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/udi_composite_desc.c
@@ -187,5 +187,6 @@ UDC_DESC_STORAGE udc_config_t udc_config = {
 /**INDENT-ON**/
 //@}
 
-#endif
-#endif
\ No newline at end of file
+#endif // ARDUINO_ARCH_SAM
+
+#endif // SDSUPPORT
diff --git a/Marlin/src/HAL/HAL_DUE/usb/udi_msc.c b/Marlin/src/HAL/HAL_DUE/usb/udi_msc.c
index 83d4447561..97d3f2990b 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/udi_msc.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/udi_msc.c
@@ -1127,5 +1127,6 @@ bool udi_msc_trans_block(bool b_read, uint8_t * block, iram_size_t block_size,
 
 //@}
 
-#endif
-#endif
\ No newline at end of file
+#endif // SDSUPPORT
+
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/uotghs_device_due.c b/Marlin/src/HAL/HAL_DUE/usb/uotghs_device_due.c
index 243e2db541..fce050cf69 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/uotghs_device_due.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/uotghs_device_due.c
@@ -2070,4 +2070,4 @@ static bool udd_ep_interrupt(void)
 
 //@}
 
-#endif
\ No newline at end of file
+#endif // ARDUINO_ARCH_SAM
diff --git a/Marlin/src/HAL/HAL_DUE/usb/uotghs_otg.h b/Marlin/src/HAL/HAL_DUE/usb/uotghs_otg.h
index 34436165e2..86c903b2c1 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/uotghs_otg.h
+++ b/Marlin/src/HAL/HAL_DUE/usb/uotghs_otg.h
@@ -238,5 +238,4 @@ void otg_dual_disable(void);
 }
 #endif
 
-
 #endif /* UOTGHS_OTG_H_INCLUDED */
diff --git a/Marlin/src/HAL/HAL_DUE/usb/usb_task.c b/Marlin/src/HAL/HAL_DUE/usb/usb_task.c
index 55d3e846fb..468385b508 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/usb_task.c
+++ b/Marlin/src/HAL/HAL_DUE/usb/usb_task.c
@@ -56,7 +56,7 @@
 static volatile bool main_b_cdc_enable = false;
 static volatile bool main_b_dtr_active = false;
 
-void HAL_idletask(void) {
+void usb_task_idle(void) {
   #if ENABLED(SDSUPPORT)
     // Attend SD card access from the USB MSD -- Prioritize access to improve speed
     int delay = 2;
@@ -107,8 +107,15 @@ void usb_task_cdc_set_dtr(const uint8_t port, const bool b_enable) {
 
   if (1200 == dwDTERate) {
     // We check DTR state to determine if host port is open (bit 0 of lineState).
-    if (!b_enable)
+    if (!b_enable) {
+
+      // Set RST pin to go low for 65535 clock cycles on reset
+      //  This helps restarting when firmware flash ends
+      RSTC->RSTC_MR = 0xA5000F01;
+
+      // Schedule delayed reset
       initiateReset(250);
+    }
     else
       cancelReset();
   }
@@ -290,7 +297,7 @@ bool usb_task_other_requests(void) {
   return true;
 }
 
-void HAL_init(void) {
+void usb_task_init(void) {
 
   uint16_t *ptr;
 
diff --git a/Marlin/src/HAL/HAL_DUE/usb/usb_task.h b/Marlin/src/HAL/HAL_DUE/usb/usb_task.h
index 22328e6de4..fad62fda50 100644
--- a/Marlin/src/HAL/HAL_DUE/usb/usb_task.h
+++ b/Marlin/src/HAL/HAL_DUE/usb/usb_task.h
@@ -49,6 +49,10 @@
 
 #include "usb_protocol_cdc.h"
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /*! \brief Called by MSC interface
  * Callback running when USB Host enable MSC interface
  *
@@ -111,8 +115,20 @@ void usb_task_cdc_rx_notify(const uint8_t port);
  */
 void usb_task_cdc_config(const uint8_t port, usb_cdc_line_coding_t *cfg);
 
-/* The USB device interrupt
+/*! \brief The USB device interrupt
  */
 void USBD_ISR(void);
 
-#endif // _MAIN_H_
+/*! \brief USB task init
+ */
+void usb_task_init(void);
+
+/*! \brief USB task idle
+ */
+void usb_task_idle(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif // _USB_TASK_H_
diff --git a/Marlin/src/HAL/HAL_DUE/watchdog_Due.cpp b/Marlin/src/HAL/HAL_DUE/watchdog_Due.cpp
index 329c97c557..79081f43a2 100644
--- a/Marlin/src/HAL/HAL_DUE/watchdog_Due.cpp
+++ b/Marlin/src/HAL/HAL_DUE/watchdog_Due.cpp
@@ -23,17 +23,88 @@
 #ifdef ARDUINO_ARCH_SAM
 
 #include "../../inc/MarlinConfig.h"
+#include "../../Marlin.h"
+#include "watchdog_Due.h"
+
+// Override Arduino runtime to either config or disable the watchdog
+//
+// We need to configure the watchdog as soon as possible in the boot
+// process, because watchdog initialization at hardware reset on SAM3X8E
+// is unreliable, and there is risk of unintended resets if we delay
+// that initialization to a later time.
+void watchdogSetup(void) {
+
+  #if ENABLED(USE_WATCHDOG)
+
+    // 4 seconds timeout
+    uint32_t timeout = 4000;
+
+    // Calculate timeout value in WDT counter ticks: This assumes
+    // the slow clock is running at 32.768 kHz watchdog
+    // frequency is therefore 32768 / 128 = 256 Hz
+    timeout = (timeout << 8) / 1000;
+    if (timeout == 0)
+      timeout = 1;
+    else if (timeout > 0xFFF)
+      timeout = 0xFFF;
+
+    // We want to enable the watchdog with the specified timeout
+    uint32_t value =
+      WDT_MR_WDV(timeout) |               // With the specified timeout
+      WDT_MR_WDD(timeout) |               // and no invalid write window
+    #if !(SAMV70 || SAMV71 || SAME70 || SAMS70)
+      WDT_MR_WDRPROC   |                  // WDT fault resets processor only - We want
+                                          // to keep PIO controller state
+    #endif
+      WDT_MR_WDDBGHLT  |                  // WDT stops in debug state.
+      WDT_MR_WDIDLEHLT;                   // WDT stops in idle state.
+
+    #if ENABLED(WATCHDOG_RESET_MANUAL)
+      // We enable the watchdog timer, but only for the interrupt.
+
+      // Configure WDT to only trigger an interrupt
+      value |= WDT_MR_WDFIEN;             // Enable WDT fault interrupt.
+
+      // Disable WDT interrupt (just in case, to avoid triggering it!)
+      NVIC_DisableIRQ(WDT_IRQn);
+
+      // Initialize WDT with the given parameters
+      WDT_Enable(WDT, value);
+
+      // Configure and enable WDT interrupt.
+      NVIC_ClearPendingIRQ(WDT_IRQn);
+      NVIC_SetPriority(WDT_IRQn, 0); // Use highest priority, so we detect all kinds of lockups
+      NVIC_EnableIRQ(WDT_IRQn);
+
+    #else
+
+      // a WDT fault triggers a reset
+      value |= WDT_MR_WDRSTEN;
+
+      // Initialize WDT with the given parameters
+      WDT_Enable(WDT, value);
+
+    #endif
+
+    // Reset the watchdog
+    WDT_Restart(WDT);
+
+  #else
+
+    // Make sure to completely disable the Watchdog
+    WDT_Disable(WDT);
+
+  #endif
+}
 
 #if ENABLED(USE_WATCHDOG)
-
-  #include "watchdog_Due.h"
-
-  void watchdogSetup(void) {
-    // do whatever. don't remove this function.
+  // Initialize watchdog - On SAM3X, Watchdog was already configured
+  //  and enabled or disabled at startup, so no need to reconfigure it
+  //  here.
+  void watchdog_init(void) {
+    // Reset watchdog to start clean
+    WDT_Restart(WDT);
   }
-
-  void watchdog_init(void) { watchdogEnable(4000); }
-
 #endif // USE_WATCHDOG
 
 #endif
diff --git a/Marlin/src/Marlin.cpp b/Marlin/src/Marlin.cpp
index 41672e9aae..c7ee0f407d 100644
--- a/Marlin/src/Marlin.cpp
+++ b/Marlin/src/Marlin.cpp
@@ -648,9 +648,6 @@ void setup() {
 
   #ifdef HAL_INIT
     HAL_init();
-    #if defined(ARDUINO_ARCH_SAM) && PIN_EXISTS(BEEPER) && ENABLED(SPEAKER)
-      toneInit();
-    #endif
   #endif
 
   #if ENABLED(MAX7219_DEBUG)
diff --git a/Marlin/src/inc/Conditionals_post.h b/Marlin/src/inc/Conditionals_post.h
index a440771d33..c838690aef 100644
--- a/Marlin/src/inc/Conditionals_post.h
+++ b/Marlin/src/inc/Conditionals_post.h
@@ -1396,4 +1396,7 @@
   #define HAS_FOLDER_SORTING (FOLDER_SORTING || ENABLED(SDSORT_GCODE))
 #endif
 
+// If platform requires early initialization of watchdog to properly boot
+#define EARLY_WATCHDOG (ENABLED(USE_WATCHDOG) && defined(ARDUINO_ARCH_SAM))
+
 #endif // CONDITIONALS_POST_H
diff --git a/Marlin/src/module/temperature.cpp b/Marlin/src/module/temperature.cpp
index 1f7089adc1..68feb8bd09 100644
--- a/Marlin/src/module/temperature.cpp
+++ b/Marlin/src/module/temperature.cpp
@@ -117,6 +117,10 @@ int16_t Temperature::current_temperature_raw[HOTENDS] = { 0 },
 
 // private:
 
+#if EARLY_WATCHDOG
+  bool Temperature::inited = false;
+#endif
+
 #if ENABLED(TEMP_SENSOR_1_AS_REDUNDANT)
   uint16_t Temperature::redundant_temperature_raw = 0;
   float Temperature::redundant_temperature = 0.0;
@@ -761,6 +765,14 @@ float Temperature::get_pid_output(const int8_t e) {
  */
 void Temperature::manage_heater() {
 
+  #if EARLY_WATCHDOG
+    // If thermal manager is still not running, make sure to at least reset the watchdog!
+    if (!inited) {
+      watchdog_reset();
+      return;
+    }
+  #endif
+
   #if ENABLED(PROBING_HEATERS_OFF) && ENABLED(BED_LIMIT_SWITCHING)
     static bool last_pause_state;
   #endif
@@ -1053,6 +1065,12 @@ void Temperature::updateTemperaturesFromRawValues() {
  */
 void Temperature::init() {
 
+  #if EARLY_WATCHDOG
+    // Flag that the thermalManager should be running
+    if (inited) return;
+    inited = true;
+  #endif
+
   #if MB(RUMBA) && (TEMP_SENSOR_0 == -1 || TEMP_SENSOR_1 == -1 || TEMP_SENSOR_2 == -1 || TEMP_SENSOR_BED == -1)
     // Disable RUMBA JTAG in case the thermocouple extension is plugged on top of JTAG connector
     MCUCR = _BV(JTD);
diff --git a/Marlin/src/module/temperature.h b/Marlin/src/module/temperature.h
index b92140c26a..45263b4a2f 100644
--- a/Marlin/src/module/temperature.h
+++ b/Marlin/src/module/temperature.h
@@ -202,6 +202,11 @@ class Temperature {
 
   private:
 
+    #if EARLY_WATCHDOG
+      // If temperature controller is running
+      static bool inited;
+    #endif
+
     #if ENABLED(TEMP_SENSOR_1_AS_REDUNDANT)
       static uint16_t redundant_temperature_raw;
       static float redundant_temperature;
diff --git a/Marlin/src/sd/Sd2Card.cpp b/Marlin/src/sd/Sd2Card.cpp
index da831525ef..9216480e20 100644
--- a/Marlin/src/sd/Sd2Card.cpp
+++ b/Marlin/src/sd/Sd2Card.cpp
@@ -260,6 +260,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
   // must supply min of 74 clock cycles with CS high.
   for (uint8_t i = 0; i < 10; i++) spiSend(0xFF);
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // command to go idle in SPI mode
   while ((status_ = cardCommand(CMD0, 0)) != R1_IDLE_STATE) {
     if (((uint16_t)millis() - t0) > SD_INIT_TIMEOUT) {
@@ -272,6 +277,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
     crcSupported = (cardCommand(CMD59, 1) == R1_IDLE_STATE);
   #endif
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // check SD version
   for (;;) {
     if (cardCommand(CMD8, 0x1AA) == (R1_ILLEGAL_COMMAND | R1_IDLE_STATE)) {
@@ -292,6 +302,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
     }
   }
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // initialize card and send host supports SDHC if SD2
   arg = type() == SD_CARD_TYPE_SD2 ? 0x40000000 : 0;
   while ((status_ = cardAcmd(ACMD41, arg)) != R1_READY_STATE) {