diff --git a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
index aba3b3270a..9d2233d914 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
+++ b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.cpp
@@ -63,8 +63,8 @@
 const tTimerConfig TimerConfig [NUM_HARDWARE_TIMERS] = {
   { TC0, 0, TC0_IRQn,  3}, // 0 - [servo timer5]
   { TC0, 1, TC1_IRQn,  0}, // 1
-  { TC0, 2, TC2_IRQn,  0}, // 2
-  { TC1, 0, TC3_IRQn,  2}, // 3 - stepper
+  { TC0, 2, TC2_IRQn,  2}, // 2 - stepper
+  { TC1, 0, TC3_IRQn,  0}, // 3
   { TC1, 1, TC4_IRQn, 15}, // 4 - temperature
   { TC1, 2, TC5_IRQn,  3}, // 5 - [servo timer3]
   { TC2, 0, TC6_IRQn, 14}, // 6 - tone
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
index 1b002469be..a2676e0875 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
+++ b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
@@ -43,7 +43,7 @@ typedef uint32_t hal_timer_t;
 
 #define HAL_TIMER_RATE         ((F_CPU) / 2)    // frequency of timers peripherals
 
-#define STEP_TIMER_NUM 3  // index of timer to use for stepper
+#define STEP_TIMER_NUM 2  // index of timer to use for stepper
 #define TEMP_TIMER_NUM 4  // index of timer to use for temperature
 #define PULSE_TIMER_NUM STEP_TIMER_NUM
 #define TONE_TIMER_NUM 6  // index of timer to use for beeper tones
@@ -65,7 +65,7 @@ typedef uint32_t hal_timer_t;
 #define ENABLE_TEMPERATURE_INTERRUPT()  HAL_timer_enable_interrupt(TEMP_TIMER_NUM)
 #define DISABLE_TEMPERATURE_INTERRUPT() HAL_timer_disable_interrupt(TEMP_TIMER_NUM)
 
-#define HAL_STEP_TIMER_ISR()  void TC3_Handler()
+#define HAL_STEP_TIMER_ISR()  void TC2_Handler()
 #define HAL_TEMP_TIMER_ISR()  void TC4_Handler()
 #define HAL_TONE_TIMER_ISR()  void TC6_Handler()