diff --git a/ports/atmel-samd/common-hal/audioio/AudioOut.c b/ports/atmel-samd/common-hal/audioio/AudioOut.c
index fb9ef00af1..a75abd324b 100644
--- a/ports/atmel-samd/common-hal/audioio/AudioOut.c
+++ b/ports/atmel-samd/common-hal/audioio/AudioOut.c
@@ -252,7 +252,8 @@ void common_hal_audioio_audioout_construct(audioio_audioout_obj_t* self,
     tc_gclk = 1;
     #endif
 
-    turn_on_clocks(true, tc_index, tc_gclk, TC_HANDLER_NO_INTERRUPT);
+    set_timer_handler(true, tc_index, TC_HANDLER_NO_INTERRUPT);
+    turn_on_clocks(true, tc_index, tc_gclk);
 
     // Don't bother setting the period. We set it before you playback anything.
     tc_set_enable(t, false);
diff --git a/ports/atmel-samd/common-hal/pulseio/PWMOut.c b/ports/atmel-samd/common-hal/pulseio/PWMOut.c
index dcc2363323..19daaa14fd 100644
--- a/ports/atmel-samd/common-hal/pulseio/PWMOut.c
+++ b/ports/atmel-samd/common-hal/pulseio/PWMOut.c
@@ -235,8 +235,9 @@ pwmout_result_t common_hal_pulseio_pwmout_construct(pulseio_pwmout_obj_t* self,
             }
         }
 
+        set_timer_handler(timer->is_tc, timer->index, TC_HANDLER_NO_INTERRUPT);
         // We use the zeroeth clock on either port to go full speed.
-        turn_on_clocks(timer->is_tc, timer->index, 0, TC_HANDLER_NO_INTERRUPT);
+        turn_on_clocks(timer->is_tc, timer->index, 0);
 
         if (timer->is_tc) {
             tc_periods[timer->index] = top;
diff --git a/ports/atmel-samd/common-hal/pulseio/PulseOut.c b/ports/atmel-samd/common-hal/pulseio/PulseOut.c
index 68f5d8fff9..528a5c808a 100644
--- a/ports/atmel-samd/common-hal/pulseio/PulseOut.c
+++ b/ports/atmel-samd/common-hal/pulseio/PulseOut.c
@@ -113,13 +113,14 @@ void common_hal_pulseio_pulseout_construct(pulseio_pulseout_obj_t* self,
 
         pulseout_tc_index = index;
 
+        set_timer_handler(true, index, TC_HANDLER_PULSEOUT);
         // We use GCLK0 for SAMD21 and GCLK1 for SAMD51 because they both run at 48mhz making our
         // math the same across the boards.
         #ifdef SAMD21
-        turn_on_clocks(true, index, 0, TC_HANDLER_PULSEOUT);
+        turn_on_clocks(true, index, 0);
         #endif
         #ifdef SAMD51
-        turn_on_clocks(true, index, 1, TC_HANDLER_PULSEOUT);
+        turn_on_clocks(true, index, 1);
         #endif
 
 
diff --git a/ports/atmel-samd/timer_handler.c b/ports/atmel-samd/timer_handler.c
index bb0d248b55..566dd8cbd0 100644
--- a/ports/atmel-samd/timer_handler.c
+++ b/ports/atmel-samd/timer_handler.c
@@ -34,8 +34,10 @@
 
 static uint8_t tc_handler[TC_INST_NUM];
 
-void set_timer_handler(uint8_t index, uint8_t timer_handler) {
-    tc_handler[index] = timer_handler;
+void set_timer_handler(bool is_tc, uint8_t index, uint8_t timer_handler) {
+    if (is_tc) {
+        tc_handler[index] = timer_handler;
+    }
 }
 
 void shared_timer_handler(bool is_tc, uint8_t index) {
diff --git a/ports/atmel-samd/timer_handler.h b/ports/atmel-samd/timer_handler.h
index 3243740e24..a495e21f2a 100644
--- a/ports/atmel-samd/timer_handler.h
+++ b/ports/atmel-samd/timer_handler.h
@@ -30,7 +30,7 @@
 #define TC_HANDLER_PULSEOUT 0x1
 #define TC_HANDLER_FREQUENCYIN 0x2
 
-void set_timer_handler(uint8_t index, uint8_t timer_handler);
+void set_timer_handler(bool is_tc, uint8_t index, uint8_t timer_handler);
 void shared_timer_handler(bool is_tc, uint8_t index);
 
 #endif  // MICROPY_INCLUDED_ATMEL_SAMD_TIMER_HANDLER_H