diff --git a/sdks/go/pkg/beam/runners/prism/internal/engine/elementmanager.go b/sdks/go/pkg/beam/runners/prism/internal/engine/elementmanager.go
index de997fa3282c..08056ae18b22 100644
--- a/sdks/go/pkg/beam/runners/prism/internal/engine/elementmanager.go
+++ b/sdks/go/pkg/beam/runners/prism/internal/engine/elementmanager.go
@@ -53,6 +53,7 @@ type element struct {
 	// No synchronization is required in specifying this,
 	// since keyed elements are only processed by a single bundle at a time,
 	// if stateful stages are concerned.
+	// If a timer element has sequence set to -1, it means it is being cleared.
 	sequence int
 
 	elmBytes []byte // When nil, indicates this is a timer.
@@ -959,11 +960,6 @@ func (em *ElementManager) triageTimers(d TentativeData, inputInfo PColInfo, stag
 				for _, e := range ret.elms {
 					keyToTimers[timerKey{key: string(ret.keyBytes), tag: ret.tag, win: e.window}] = e
 				}
-				if len(ret.elms) == 0 {
-					for _, w := range ret.windows {
-						delete(keyToTimers, timerKey{key: string(ret.keyBytes), tag: ret.tag, win: w})
-					}
-				}
 				// Indicate we'd like to continue iterating.
 				return true
 			})
@@ -1347,16 +1343,23 @@ func (*statefulStageKind) addPending(ss *stageState, em *ElementManager, newPend
 		if e.IsTimer() {
 			if lastSet, ok := dnt.timers[timerKey{family: e.family, tag: e.tag, window: e.window}]; ok {
 				// existing timer!
-				// don't increase the count this time, as "this" timer is already pending.
+				// don't increase the count this time, as "e" is already pending.
 				count--
 				// clear out the existing hold for accounting purposes.
 				ss.watermarkHolds.Drop(lastSet.hold, 1)
 			}
-			// Update the last set time on the timer.
-			dnt.timers[timerKey{family: e.family, tag: e.tag, window: e.window}] = timerTimes{firing: e.timestamp, hold: e.holdTimestamp}
+			if e.sequence >= 0 {
+				// Update the last set time on the timer.
+				dnt.timers[timerKey{family: e.family, tag: e.tag, window: e.window}] = timerTimes{firing: e.timestamp, hold: e.holdTimestamp}
 
-			// Mark the hold in the heap.
-			ss.watermarkHolds.Add(e.holdTimestamp, 1)
+				// Mark the hold in the heap.
+				ss.watermarkHolds.Add(e.holdTimestamp, 1)
+			} else {
+				// decrement the pending count since "e" is not a real timer (merely a clearing signal)
+				count--
+				// timer is to be cleared
+				delete(dnt.timers, timerKey{family: e.family, tag: e.tag, window: e.window})
+			}
 		}
 	}
 	return count
diff --git a/sdks/go/pkg/beam/runners/prism/internal/engine/timers.go b/sdks/go/pkg/beam/runners/prism/internal/engine/timers.go
index 8b90591974b8..636ed5a644cc 100644
--- a/sdks/go/pkg/beam/runners/prism/internal/engine/timers.go
+++ b/sdks/go/pkg/beam/runners/prism/internal/engine/timers.go
@@ -86,8 +86,19 @@ func decodeTimerIter(keyDec func(io.Reader) []byte, winCoder WinCoderType, raw [
 			clear := d.Bool()
 			hold := mtime.MaxTimestamp
 			if clear {
-				if !yield(timerRet{keyBytes, tag, nil, ws}) {
-					return // Halt iteration if yeild returns false.
+				var elms []element
+				for _, w := range ws {
+					elms = append(elms, element{
+						tag:      tag,
+						elmBytes: nil, // indicates this is a timer.
+						keyBytes: keyBytes,
+						window:   w,
+						sequence: -1, // indicates this timer is being cleared.
+					})
+				}
+
+				if !yield(timerRet{keyBytes, tag, elms, ws}) {
+					return // Halt iteration if yield returns false.
 				}
 				// Otherwise continue handling the remaining bytes.
 				raw = d.UnusedBytes()
@@ -113,7 +124,7 @@ func decodeTimerIter(keyDec func(io.Reader) []byte, winCoder WinCoderType, raw [
 			}
 
 			if !yield(timerRet{keyBytes, tag, elms, ws}) {
-				return // Halt iteration if yeild returns false.
+				return // Halt iteration if yield returns false.
 			}
 			// Otherwise continue handling the remaining bytes.
 			raw = d.UnusedBytes()