diff --git a/quantum/encoder.c b/quantum/encoder.c
index 77261c6d65f2..453130ba4330 100644
--- a/quantum/encoder.c
+++ b/quantum/encoder.c
@@ -5,6 +5,7 @@
 #include "action.h"
 #include "encoder.h"
 #include "wait.h"
+#include "debug.h"
 
 #ifndef ENCODER_MAP_KEY_DELAY
 #    define ENCODER_MAP_KEY_DELAY TAP_CODE_DELAY
@@ -15,12 +16,19 @@ __attribute__((weak)) bool should_process_encoder(void) {
 }
 
 static encoder_events_t encoder_events;
+static bool             signal_queue_drain = false;
 
 void encoder_init(void) {
     memset(&encoder_events, 0, sizeof(encoder_events));
     encoder_driver_init();
 }
 
+static void encoder_queue_drain(void) {
+    // dprintf("Draining encoder queue\n");
+    encoder_events.tail     = encoder_events.head;
+    encoder_events.dequeued = encoder_events.enqueued;
+}
+
 static bool encoder_handle_queue(void) {
     bool    changed = false;
     uint8_t index;
@@ -60,6 +68,11 @@ bool encoder_task(void) {
     }
 #endif // SPLIT_KEYBOARD
 
+    if (signal_queue_drain) {
+        signal_queue_drain = false;
+        encoder_queue_drain();
+    }
+
     // Let the encoder driver produce events
     encoder_driver_task();
 
@@ -137,18 +150,9 @@ void encoder_retrieve_events(encoder_events_t *events) {
     memcpy(events, &encoder_events, sizeof(encoder_events));
 }
 
-#ifdef SPLIT_KEYBOARD
-void encoder_queue_drain(void) {
-    uint8_t index;
-    bool    clockwise;
-
-    // dprintf("Draining encoder queue\n");
-
-    while (encoder_events.dequeued != encoder_events.enqueued) {
-        encoder_dequeue_event(&index, &clockwise);
-    }
+void encoder_signal_queue_drain(void) {
+    signal_queue_drain = true;
 }
-#endif // SPLIT_KEYBOARD
 
 __attribute__((weak)) bool encoder_update_user(uint8_t index, bool clockwise) {
     return true;
diff --git a/quantum/encoder.h b/quantum/encoder.h
index 8d735bfc64ba..317a91f1da54 100644
--- a/quantum/encoder.h
+++ b/quantum/encoder.h
@@ -83,8 +83,8 @@ typedef struct encoder_event_t {
 } encoder_event_t;
 
 typedef struct encoder_events_t {
-    uint16_t        enqueued;
-    uint16_t        dequeued;
+    uint8_t         enqueued;
+    uint8_t         dequeued;
     uint8_t         head;
     uint8_t         tail;
     encoder_event_t queue[MAX_QUEUED_ENCODER_EVENTS];
@@ -97,9 +97,8 @@ void encoder_retrieve_events(encoder_events_t *events);
 bool encoder_queue_event_advanced(encoder_events_t *events, uint8_t index, bool clockwise);
 bool encoder_dequeue_event_advanced(encoder_events_t *events, uint8_t *index, bool *clockwise);
 
-#    ifdef SPLIT_KEYBOARD
-void encoder_queue_drain(void);
-#    endif // SPLIT_KEYBOARD
+// Reset the queue to be empty
+void encoder_signal_queue_drain(void);
 
 #    ifdef ENCODER_MAP_ENABLE
 #        define NUM_DIRECTIONS 2
diff --git a/quantum/split_common/transactions.c b/quantum/split_common/transactions.c
index 4a385cffcaa3..33bc9e9f575a 100644
--- a/quantum/split_common/transactions.c
+++ b/quantum/split_common/transactions.c
@@ -14,6 +14,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <stdint.h>
 #include <string.h>
 #include <stddef.h>
 
@@ -238,21 +239,25 @@ static void master_matrix_handlers_slave(matrix_row_t master_matrix[], matrix_ro
 #ifdef ENCODER_ENABLE
 
 static bool encoder_handlers_master(matrix_row_t master_matrix[], matrix_row_t slave_matrix[]) {
-    static uint32_t  last_update = 0;
+    static uint32_t  last_update   = 0;
+    static uint8_t   last_checksum = 0;
     encoder_events_t temp_events;
 
     bool okay = read_if_checksum_mismatch(GET_ENCODERS_CHECKSUM, GET_ENCODERS_DATA, &last_update, &temp_events, &split_shmem->encoders.events, sizeof(temp_events));
     if (okay) {
-        bool    actioned = false;
-        uint8_t index;
-        bool    clockwise;
-        while (okay && encoder_dequeue_event_advanced(&split_shmem->encoders.events, &index, &clockwise)) {
-            okay &= encoder_queue_event(index, clockwise);
-            actioned = true;
-        }
+        if (last_checksum != split_shmem->encoders.checksum) {
+            bool    actioned = false;
+            uint8_t index;
+            bool    clockwise;
+            while (okay && encoder_dequeue_event_advanced(&split_shmem->encoders.events, &index, &clockwise)) {
+                okay &= encoder_queue_event(index, clockwise);
+                actioned = true;
+            }
 
-        if (actioned) {
-            transport_exec(CMD_ENCODER_DRAIN);
+            if (actioned) {
+                okay &= transport_exec(CMD_ENCODER_DRAIN);
+            }
+            last_checksum = split_shmem->encoders.checksum;
         }
     }
     return okay;
@@ -266,7 +271,7 @@ static void encoder_handlers_slave(matrix_row_t master_matrix[], matrix_row_t sl
 }
 
 static void encoder_handlers_slave_drain(uint8_t initiator2target_buffer_size, const void *initiator2target_buffer, uint8_t target2initiator_buffer_size, void *target2initiator_buffer) {
-    encoder_queue_drain();
+    encoder_signal_queue_drain();
 }
 
 // clang-format off