diff --git a/Marlin/src/HAL/SAMD51/timers.cpp b/Marlin/src/HAL/SAMD51/timers.cpp
index 3eb021c25..158ea4ed1 100644
--- a/Marlin/src/HAL/SAMD51/timers.cpp
+++ b/Marlin/src/HAL/SAMD51/timers.cpp
@@ -121,14 +121,15 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency) {
     tc->COUNT32.CTRLA.bit.SWRST = true;
     SYNC(tc->COUNT32.SYNCBUSY.bit.SWRST);
 
-    // Wave mode, reset counter on overflow on 0 (I use count down to prevent double buffer use)
+    // Wave mode, reset counter on compare match
     tc->COUNT32.WAVE.reg = TC_WAVE_WAVEGEN_MFRQ;
     tc->COUNT32.CTRLA.reg = TC_CTRLA_MODE_COUNT32 | TC_CTRLA_PRESCALER_DIV1;
-    tc->COUNT32.CTRLBSET.reg = TC_CTRLBCLR_DIR;
+    tc->COUNT32.CTRLBCLR.reg = TC_CTRLBCLR_DIR;
     SYNC(tc->COUNT32.SYNCBUSY.bit.CTRLB);
 
     // Set compare value
-    tc->COUNT32.COUNT.reg = tc->COUNT32.CC[0].reg = (HAL_TIMER_RATE) / frequency;
+    tc->COUNT32.CC[0].reg = (HAL_TIMER_RATE) / frequency;
+    tc->COUNT32.COUNT.reg = 0;
 
     // Enable interrupt on compare
     tc->COUNT32.INTFLAG.reg = TC_INTFLAG_OVF;   // reset pending interrupt
diff --git a/Marlin/src/HAL/SAMD51/timers.h b/Marlin/src/HAL/SAMD51/timers.h
index 4b21e4716..69793ea58 100644
--- a/Marlin/src/HAL/SAMD51/timers.h
+++ b/Marlin/src/HAL/SAMD51/timers.h
@@ -97,13 +97,13 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency);
 FORCE_INLINE static void HAL_timer_set_compare(const uint8_t timer_num, const hal_timer_t compare) {
   // Should never be called with timer RTC_TIMER_NUM
   Tc * const tc = TimerConfig[timer_num].pTc;
-  tc->COUNT32.CC[0].reg = HAL_TIMER_TYPE_MAX - compare;
+  tc->COUNT32.CC[0].reg = compare;
 }
 
 FORCE_INLINE static hal_timer_t HAL_timer_get_compare(const uint8_t timer_num) {
   // Should never be called with timer RTC_TIMER_NUM
   Tc * const tc = TimerConfig[timer_num].pTc;
-  return (hal_timer_t)(HAL_TIMER_TYPE_MAX - tc->COUNT32.CC[0].reg);
+  return (hal_timer_t)tc->COUNT32.CC[0].reg;
 }
 
 FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
@@ -111,7 +111,7 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
   Tc * const tc = TimerConfig[timer_num].pTc;
   tc->COUNT32.CTRLBSET.reg = TC_CTRLBCLR_CMD_READSYNC;
   SYNC(tc->COUNT32.SYNCBUSY.bit.CTRLB || tc->COUNT32.SYNCBUSY.bit.COUNT);
-  return HAL_TIMER_TYPE_MAX - tc->COUNT32.COUNT.reg;
+  return tc->COUNT32.COUNT.reg;
 }
 
 void HAL_timer_enable_interrupt(const uint8_t timer_num);