diff --git a/Marlin/src/HAL/HAL_AVR/HAL_AVR.h b/Marlin/src/HAL/HAL_AVR/HAL_AVR.h
index 6c6b9be0b5..2d59323051 100644
--- a/Marlin/src/HAL/HAL_AVR/HAL_AVR.h
+++ b/Marlin/src/HAL/HAL_AVR/HAL_AVR.h
@@ -100,30 +100,39 @@ extern "C" {
 
 
 // timers
-#define STEP_TIMER_NUM OCR1A
-#define TEMP_TIMER_NUM 0
-#define TEMP_TIMER_FREQUENCY (F_CPU / 64.0 / 256.0)
-
 #define HAL_TIMER_RATE          ((F_CPU) / 8)    // i.e., 2MHz or 2.5MHz
-#define HAL_STEPPER_TIMER_RATE  HAL_TIMER_RATE
-#define STEPPER_TIMER_PRESCALE  INT0_PRESCALER
 #define HAL_TICKS_PER_US        ((HAL_STEPPER_TIMER_RATE) / 1000000) // Cannot be of type double
 
+#define TEMP_TIMER_FREQUENCY    ((F_CPU) / 64.0 / 256.0)
+
+#define HAL_STEPPER_TIMER_RATE  HAL_TIMER_RATE
+#define STEPPER_TIMER_PRESCALE  8
+
+#define STEP_TIMER_NUM          1
+#define TIMER_OCR_1             OCR1A
+#define TIMER_COUNTER_1         TCNT1
+
+#define TEMP_TIMER_NUM          0
+#define TIMER_OCR_0             OCR0A
+#define TIMER_COUNTER_0         TCNT0
+
+#define PULSE_TIMER_NUM         TEMP_TIMER_NUM
+#define PULSE_TIMER_PRESCALE    8
+
 #define ENABLE_STEPPER_DRIVER_INTERRUPT()  SBI(TIMSK1, OCIE1A)
 #define DISABLE_STEPPER_DRIVER_INTERRUPT() CBI(TIMSK1, OCIE1A)
 
 #define ENABLE_TEMPERATURE_INTERRUPT()  SBI(TIMSK0, OCIE0B)
 #define DISABLE_TEMPERATURE_INTERRUPT() CBI(TIMSK0, OCIE0B)
 
-//void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency);
-#define HAL_timer_start(timer_num,frequency)
-
-//void HAL_timer_set_count(const uint8_t timer_num, const uint16_t count);
-#define HAL_timer_set_count(timer, count) timer = (count)
+#define HAL_timer_start(timer_num, frequency)
 
-#define HAL_timer_get_current_count(timer) timer
+#define _CAT(a, ...) a ## __VA_ARGS__
+#define HAL_timer_set_count(timer, count) (_CAT(TIMER_OCR_, timer) = count)
+#define HAL_timer_get_count(timer) _CAT(TIMER_OCR_, timer)
+#define HAL_timer_set_current_count(timer, count) (_CAT(TIMER_COUNTER_, timer) = count)
+#define HAL_timer_get_current_count(timer) _CAT(TIMER_COUNTER_, timer)
 
-//void HAL_timer_isr_prologue(const uint8_t timer_num);
 #define HAL_timer_isr_prologue(timer_num)
 
 #define HAL_STEP_TIMER_ISR ISR(TIMER1_COMPA_vect)
diff --git a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
index 2d70792061..b93e80b7d6 100644
--- a/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
+++ b/Marlin/src/HAL/HAL_DUE/HAL_timers_Due.h
@@ -64,6 +64,9 @@ typedef uint32_t hal_timer_t;
 #define HAL_STEP_TIMER_ISR  void TC3_Handler()
 #define HAL_TEMP_TIMER_ISR  void TC4_Handler()
 
+#define PULSE_TIMER_NUM STEP_TIMER_NUM
+#define PULSE_TIMER_PRESCALE STEPPER_TIMER_PRESCALE
+
 // --------------------------------------------------------------------------
 // Types
 // --------------------------------------------------------------------------
@@ -87,7 +90,7 @@ extern const tTimerConfig TimerConfig[];
 
 void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency);
 
-FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const uint32_t count) {
+FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const hal_timer_t count) {
   const tTimerConfig *pConfig = &TimerConfig[timer_num];
   pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_RC = count;
 }
@@ -97,7 +100,12 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
   return pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_RC;
 }
 
-FORCE_INLINE static uint32_t HAL_timer_get_current_count(const uint8_t timer_num) {
+FORCE_INLINE static void HAL_timer_set_current_count(const uint8_t timer_num, const hal_timer_t count) {
+  const tTimerConfig *pConfig = &TimerConfig[timer_num];
+  pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_CV = count;
+}
+
+FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(const uint8_t timer_num) {
   const tTimerConfig *pConfig = &TimerConfig[timer_num];
   return pConfig->pTimerRegs->TC_CHANNEL[pConfig->channel].TC_CV;
 }
diff --git a/Marlin/src/HAL/HAL_LPC1768/HAL_timers.h b/Marlin/src/HAL/HAL_LPC1768/HAL_timers.h
index 52ee1f7d36..15085efa60 100644
--- a/Marlin/src/HAL/HAL_LPC1768/HAL_timers.h
+++ b/Marlin/src/HAL/HAL_LPC1768/HAL_timers.h
@@ -53,6 +53,9 @@ typedef uint32_t hal_timer_t;
 #define HAL_TEMP_TIMER_RATE    1000000
 #define TEMP_TIMER_FREQUENCY   1000 // temperature interrupt frequency
 
+#define PULSE_TIMER_NUM STEP_TIMER_NUM
+#define PULSE_TIMER_PRESCALE STEPPER_TIMER_PRESCALE
+
 #define ENABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_enable_interrupt(STEP_TIMER_NUM)
 #define DISABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_disable_interrupt(STEP_TIMER_NUM)
 #define ENABLE_TEMPERATURE_INTERRUPT() HAL_timer_enable_interrupt(TEMP_TIMER_NUM)
@@ -100,6 +103,13 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
   return 0;
 }
 
+FORCE_INLINE static void HAL_timer_set_current_count(const uint8_t timer_num, const hal_timer_t count) {
+  switch (timer_num) {
+    case 0: LPC_TIM0->TC = count; break;
+    case 1: LPC_TIM1->TC = count; break;
+  }
+}
+
 FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(const uint8_t timer_num) {
   switch (timer_num) {
     case 0: return LPC_TIM0->TC;
diff --git a/Marlin/src/HAL/HAL_STM32F1/HAL_timers_Stm32f1.h b/Marlin/src/HAL/HAL_STM32F1/HAL_timers_Stm32f1.h
index 163eb498da..541a214a7a 100644
--- a/Marlin/src/HAL/HAL_STM32F1/HAL_timers_Stm32f1.h
+++ b/Marlin/src/HAL/HAL_STM32F1/HAL_timers_Stm32f1.h
@@ -51,20 +51,22 @@ typedef uint16_t hal_timer_t;
 #define TEMP_TIMER_NUM 2  // index of timer to use for temperature
 #define TEMP_TIMER_CHAN 1 // Channel of the timer to use for compare and interrupts
 
-
 #define HAL_TIMER_RATE         (F_CPU)  // frequency of timers peripherals
 #define STEPPER_TIMER_PRESCALE 36             // prescaler for setting stepper timer, 2Mhz
 #define HAL_STEPPER_TIMER_RATE (HAL_TIMER_RATE / STEPPER_TIMER_PRESCALE)   // frequency of stepper timer (HAL_TIMER_RATE / STEPPER_TIMER_PRESCALE)
 #define HAL_TICKS_PER_US       ((HAL_STEPPER_TIMER_RATE) / 1000000) // stepper timer ticks per us
 
+#define PULSE_TIMER_NUM STEP_TIMER_NUM
+#define PULSE_TIMER_PRESCALE STEPPER_TIMER_PRESCALE
+
 #define TEMP_TIMER_PRESCALE     1000 // prescaler for setting Temp timer, 72Khz
 #define TEMP_TIMER_FREQUENCY    1000 // temperature interrupt frequency
 
-#define ENABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_enable_interrupt (STEP_TIMER_NUM)
-#define DISABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_disable_interrupt (STEP_TIMER_NUM)
+#define ENABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_enable_interrupt(STEP_TIMER_NUM)
+#define DISABLE_STEPPER_DRIVER_INTERRUPT() HAL_timer_disable_interrupt(STEP_TIMER_NUM)
 
-#define ENABLE_TEMPERATURE_INTERRUPT() HAL_timer_enable_interrupt (TEMP_TIMER_NUM)
-#define DISABLE_TEMPERATURE_INTERRUPT() HAL_timer_disable_interrupt (TEMP_TIMER_NUM)
+#define ENABLE_TEMPERATURE_INTERRUPT() HAL_timer_enable_interrupt(TEMP_TIMER_NUM)
+#define DISABLE_TEMPERATURE_INTERRUPT() HAL_timer_disable_interrupt(TEMP_TIMER_NUM)
 
 #define HAL_ENABLE_ISRs() do { if (thermalManager.in_temp_isr)DISABLE_TEMPERATURE_INTERRUPT(); else ENABLE_TEMPERATURE_INTERRUPT(); ENABLE_STEPPER_DRIVER_INTERRUPT(); } while(0)
 // TODO change this
@@ -92,7 +94,7 @@ static HardwareTimer TempTimer(TEMP_TIMER_NUM);
 // Public functions
 // --------------------------------------------------------------------------
 
-void HAL_timer_start (uint8_t timer_num, uint32_t frequency);
+void HAL_timer_start(uint8_t timer_num, uint32_t frequency);
 void HAL_timer_enable_interrupt(uint8_t timer_num);
 void HAL_timer_disable_interrupt(uint8_t timer_num);
 
@@ -107,26 +109,26 @@ void HAL_timer_disable_interrupt(uint8_t timer_num);
  * Todo: Look at that possibility later.
  */
 
-FORCE_INLINE static void HAL_timer_set_count (uint8_t timer_num, uint32_t count) {
+FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const hal_timer_t count) {
   switch (timer_num) {
   case STEP_TIMER_NUM:
     StepperTimer.pause();
-    StepperTimer.setCompare (STEP_TIMER_CHAN, count);
-    StepperTimer.refresh ();
-    StepperTimer.resume ();
+    StepperTimer.setCompare(STEP_TIMER_CHAN, count);
+    StepperTimer.refresh();
+    StepperTimer.resume();
     break;
   case TEMP_TIMER_NUM:
     TempTimer.pause();
-    TempTimer.setCompare (TEMP_TIMER_CHAN, count);
-    TempTimer.refresh ();
-    TempTimer.resume ();
+    TempTimer.setCompare(TEMP_TIMER_CHAN, count);
+    TempTimer.refresh();
+    TempTimer.resume();
     break;
   default:
     break;
   }
 }
 
-FORCE_INLINE static hal_timer_t HAL_timer_get_count (uint8_t timer_num) {
+FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
   hal_timer_t temp;
   switch (timer_num) {
   case STEP_TIMER_NUM:
@@ -142,7 +144,14 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_count (uint8_t timer_num) {
   return temp;
 }
 
-FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(uint8_t timer_num) {
+FORCE_INLINE static void HAL_timer_set_current_count(const uint8_t timer_num, const hal_timer_t count) {
+  switch (timer_num) {
+    case STEP_TIMER_NUM: StepperTimer.setCount(count); break;
+    case TEMP_TIMER_NUM: TempTimer.setCount(count); break;
+  }
+}
+
+FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(const uint8_t timer_num) {
   hal_timer_t temp;
   switch (timer_num) {
   case STEP_TIMER_NUM:
@@ -158,10 +167,9 @@ FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(uint8_t timer_num) {
   return temp;
 }
 
+//void HAL_timer_isr_prologue (const uint8_t timer_num);
 
-//void HAL_timer_isr_prologue (uint8_t timer_num);
-
-FORCE_INLINE static void HAL_timer_isr_prologue(uint8_t timer_num) {
+FORCE_INLINE static void HAL_timer_isr_prologue(const uint8_t timer_num) {
   switch (timer_num) {
   case STEP_TIMER_NUM:
     StepperTimer.pause();
diff --git a/Marlin/src/HAL/HAL_TEENSY35_36/HAL_timers_Teensy.h b/Marlin/src/HAL/HAL_TEENSY35_36/HAL_timers_Teensy.h
index 65ea165615..3675ea60bd 100644
--- a/Marlin/src/HAL/HAL_TEENSY35_36/HAL_timers_Teensy.h
+++ b/Marlin/src/HAL/HAL_TEENSY35_36/HAL_timers_Teensy.h
@@ -57,6 +57,9 @@ typedef uint32_t hal_timer_t;
 #define STEPPER_TIMER STEP_TIMER_NUM // Alias?
 #define STEPPER_TIMER_PRESCALE 0 // Not defined anywhere else!
 
+#define PULSE_TIMER_NUM STEP_TIMER_NUM
+#define PULSE_TIMER_PRESCALE STEPPER_TIMER_PRESCALE
+
 #define HAL_TIMER_RATE         (FTM0_TIMER_RATE)
 #define HAL_STEPPER_TIMER_RATE HAL_TIMER_RATE
 #define HAL_TICKS_PER_US       ((HAL_STEPPER_TIMER_RATE) / 1000000)
@@ -75,23 +78,30 @@ typedef uint32_t hal_timer_t;
 
 void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency);
 
-FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const uint32_t count) {
-  switch(timer_num) {
+FORCE_INLINE static void HAL_timer_set_count(const uint8_t timer_num, const hal_timer_t count) {
+  switch (timer_num) {
     case 0: FTM0_C0V = count; break;
     case 1: FTM1_C0V = count; break;
   }
 }
 
 FORCE_INLINE static hal_timer_t HAL_timer_get_count(const uint8_t timer_num) {
-  switch(timer_num) {
+  switch (timer_num) {
     case 0: return FTM0_C0V;
     case 1: return FTM1_C0V;
   }
   return 0;
 }
 
-FORCE_INLINE static uint32_t HAL_timer_get_current_count(const uint8_t timer_num) {
-  switch(timer_num) {
+FORCE_INLINE static void HAL_timer_set_current_count(const uint8_t timer_num, const hal_timer_t count) {
+  switch (timer_num) {
+    case 0: FTM0_CNT = count;
+    case 1: FTM1_CNT = count;
+  }
+}
+
+FORCE_INLINE static hal_timer_t HAL_timer_get_current_count(const uint8_t timer_num) {
+  switch (timer_num) {
     case 0: return FTM0_CNT;
     case 1: return FTM1_CNT;
   }
diff --git a/Marlin/src/core/macros.h b/Marlin/src/core/macros.h
index aed0850215..ea6ef387b5 100644
--- a/Marlin/src/core/macros.h
+++ b/Marlin/src/core/macros.h
@@ -44,8 +44,7 @@
 #define _O3          __attribute__((optimize("O3")))
 
 // Clock speed factors
-#define CYCLES_PER_MICROSECOND (F_CPU / 1000000L) // 16 or 20
-#define INT0_PRESCALER 8
+#define CYCLES_PER_MICROSECOND (F_CPU / 1000000L) // 16 or 20 on AVR
 
 // Highly granular delays for step pulses, etc.
 #define DELAY_0_NOP NOOP
diff --git a/Marlin/src/module/stepper.cpp b/Marlin/src/module/stepper.cpp
index 77da0b26fd..cbb227d936 100644
--- a/Marlin/src/module/stepper.cpp
+++ b/Marlin/src/module/stepper.cpp
@@ -408,10 +408,13 @@ void Stepper::isr() {
   }
 
   // If there is no current block, attempt to pop one from the buffer
+  bool first_step = false;
   if (!current_block) {
     // Anything in the buffer?
     if ((current_block = planner.get_current_block())) {
       trapezoid_generator_reset();
+      HAL_timer_set_current_count(STEP_TIMER_NUM, 0);
+      first_step = true;
 
       // Initialize Bresenham counters to 1/2 the ceiling
       counter_X = counter_Y = counter_Z = counter_E = -(current_block->step_event_count >> 1);
@@ -564,7 +567,7 @@ void Stepper::isr() {
      * 10µs = 160 or 200 cycles.
      */
     #if EXTRA_CYCLES_XYZE > 20
-      hal_timer_t pulse_start = HAL_timer_get_current_count(STEP_TIMER_NUM);
+      hal_timer_t pulse_start = HAL_timer_get_current_count(PULSE_TIMER_NUM);
     #endif
 
     #if HAS_X_STEP
@@ -596,8 +599,8 @@ void Stepper::isr() {
 
     // For minimum pulse time wait before stopping pulses
     #if EXTRA_CYCLES_XYZE > 20
-      while (EXTRA_CYCLES_XYZE > (uint32_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (STEPPER_TIMER_PRESCALE)) { /* nada */ }
-      pulse_start = HAL_timer_get_current_count(STEP_TIMER_NUM);
+      while (EXTRA_CYCLES_XYZE > (uint32_t)(HAL_timer_get_current_count(PULSE_TIMER_NUM) - pulse_start) * (PULSE_TIMER_PRESCALE)) { /* nada */ }
+      pulse_start = HAL_timer_get_current_count(PULSE_TIMER_NUM);
     #elif EXTRA_CYCLES_XYZE > 0
       DELAY_NOPS(EXTRA_CYCLES_XYZE);
     #endif
@@ -637,7 +640,7 @@ void Stepper::isr() {
 
     // For minimum pulse time wait after stopping pulses also
     #if EXTRA_CYCLES_XYZE > 20
-      if (i) while (EXTRA_CYCLES_XYZE > (uint32_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (STEPPER_TIMER_PRESCALE)) { /* nada */ }
+      if (i) while (EXTRA_CYCLES_XYZE > (uint32_t)(HAL_timer_get_current_count(PULSE_TIMER_NUM) - pulse_start) * (PULSE_TIMER_PRESCALE)) { /* nada */ }
     #elif EXTRA_CYCLES_XYZE > 0
       if (i) DELAY_NOPS(EXTRA_CYCLES_XYZE);
     #endif
@@ -666,12 +669,18 @@ void Stepper::isr() {
   // Calculate new timer value
   if (step_events_completed <= (uint32_t)current_block->accelerate_until) {
 
-    #ifdef CPU_32_BIT
-      MultiU32X24toH32(acc_step_rate, acceleration_time, current_block->acceleration_rate);
-    #else
-      MultiU24X32toH16(acc_step_rate, acceleration_time, current_block->acceleration_rate);
-    #endif
-    acc_step_rate += current_block->initial_rate;
+    if (first_step) {
+      acc_step_rate = current_block->initial_rate;
+      acceleration_time = 0;
+    }
+    else {
+      #ifdef CPU_32_BIT
+        MultiU32X24toH32(acc_step_rate, acceleration_time, current_block->acceleration_rate);
+      #else
+        MultiU24X32toH16(acc_step_rate, acceleration_time, current_block->acceleration_rate);
+      #endif
+      acc_step_rate += current_block->initial_rate;
+    }
 
     // upper limit
     NOMORE(acc_step_rate, current_block->nominal_rate);
@@ -818,7 +827,7 @@ void Stepper::isr() {
     for (uint8_t i = step_loops; i--;) {
 
       #if EXTRA_CYCLES_E > 20
-        hal_timer_t pulse_start = HAL_timer_get_current_count(STEP_TIMER_NUM);
+        hal_timer_t pulse_start = HAL_timer_get_current_count(PULSE_TIMER_NUM);
       #endif
 
       START_E_PULSE(0);
@@ -837,8 +846,8 @@ void Stepper::isr() {
 
       // For minimum pulse time wait before stopping pulses
       #if EXTRA_CYCLES_E > 20
-        while (EXTRA_CYCLES_E > (hal_timer_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (STEPPER_TIMER_PRESCALE)) { /* nada */ }
-        pulse_start = HAL_timer_get_current_count(STEP_TIMER_NUM);
+        while (EXTRA_CYCLES_E > (hal_timer_t)(HAL_timer_get_current_count(PULSE_TIMER_NUM) - pulse_start) * (PULSE_TIMER_PRESCALE)) { /* nada */ }
+        pulse_start = HAL_timer_get_current_count(PULSE_TIMER_NUM);
       #elif EXTRA_CYCLES_E > 0
         DELAY_NOPS(EXTRA_CYCLES_E);
       #endif
@@ -859,7 +868,7 @@ void Stepper::isr() {
 
       // For minimum pulse time wait before looping
       #if EXTRA_CYCLES_E > 20
-        if (i) while (EXTRA_CYCLES_E > (hal_timer_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (STEPPER_TIMER_PRESCALE)) { /* nada */ }
+        if (i) while (EXTRA_CYCLES_E > (hal_timer_t)(HAL_timer_get_current_count(PULSE_TIMER_NUM) - pulse_start) * (PULSE_TIMER_PRESCALE)) { /* nada */ }
       #elif EXTRA_CYCLES_E > 0
         if (i) DELAY_NOPS(EXTRA_CYCLES_E);
       #endif
@@ -1299,7 +1308,7 @@ void Stepper::report_positions() {
 
   #if EXTRA_CYCLES_BABYSTEP > 20
     #define _SAVE_START const hal_timer_t pulse_start = HAL_timer_get_current_count(STEP_TIMER_NUM)
-    #define _PULSE_WAIT while (EXTRA_CYCLES_BABYSTEP > (uint32_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (STEPPER_TIMER_PRESCALE)) { /* nada */ }
+    #define _PULSE_WAIT while (EXTRA_CYCLES_BABYSTEP > (uint32_t)(HAL_timer_get_current_count(STEP_TIMER_NUM) - pulse_start) * (PULSE_TIMER_PRESCALE)) { /* nada */ }
   #else
     #define _SAVE_START NOOP
     #if EXTRA_CYCLES_BABYSTEP > 0
diff --git a/Marlin/src/module/stepper.h b/Marlin/src/module/stepper.h
index b15d699872..b1e73bf053 100644
--- a/Marlin/src/module/stepper.h
+++ b/Marlin/src/module/stepper.h
@@ -362,9 +362,6 @@ class Stepper {
       OCR1A_nominal = calc_timer_interval(current_block->nominal_rate);
       // make a note of the number of step loops required at nominal speed
       step_loops_nominal = step_loops;
-      acc_step_rate = current_block->initial_rate;
-      acceleration_time = calc_timer_interval(acc_step_rate);
-      _NEXT_ISR(acceleration_time);
 
       #if ENABLED(LIN_ADVANCE)
         if (current_block->use_advance_lead) {