diff --git a/server/ipqueue.go b/server/ipqueue.go
index e33d01c885..40992d7867 100644
--- a/server/ipqueue.go
+++ b/server/ipqueue.go
@@ -283,14 +283,16 @@ func (q *ipQueue[T]) size() uint64 {
 }
 
 // Empty the queue and consumes the notification signal if present.
+// Returns the number of items that were drained from the queue.
 // Note that this could cause a reader go routine that has been
 // notified that there is something in the queue (reading from queue's `ch`)
 // may then get nothing if `drain()` is invoked before the `pop()` or `popOne()`.
-func (q *ipQueue[T]) drain() {
+func (q *ipQueue[T]) drain() int {
 	if q == nil {
-		return
+		return 0
 	}
 	q.Lock()
+	olen := len(q.elts) - q.pos
 	q.elts, q.pos, q.sz = nil, 0, 0
 	// Consume the signal if it was present to reduce the chance of a reader
 	// routine to be think that there is something in the queue...
@@ -299,6 +301,7 @@ func (q *ipQueue[T]) drain() {
 	default:
 	}
 	q.Unlock()
+	return olen
 }
 
 // Since the length of the queue goes to 0 after a pop(), it is good to
diff --git a/server/jetstream_api.go b/server/jetstream_api.go
index 5b27dde28c..8a243d65d1 100644
--- a/server/jetstream_api.go
+++ b/server/jetstream_api.go
@@ -889,11 +889,13 @@ func (js *jetStream) apiDispatch(sub *subscription, c *client, acc *Account, sub
 	limit := atomic.LoadInt64(&js.queueLimit)
 retry:
 	pending, _ := s.jsAPIRoutedReqs.push(&jsAPIRoutedReq{jsub, sub, acc, subject, reply, copyBytes(rmsg), c.pa})
+	atomic.AddInt64(&js.apiInflight, 1)
 	if pending >= int(limit) {
 		if _, ok := s.jsAPIRoutedReqs.popOne(); ok {
 			// If we were able to take one of the oldest items off the queue, then
 			// retry the insert.
 			s.rateLimitFormatWarnf("JetStream API queue limit reached, dropping oldest request")
+			atomic.AddInt64(&js.apiInflight, -1)
 			s.publishAdvisory(nil, JSAdvisoryAPILimitReached, JSAPILimitReachedAdvisory{
 				TypedEvent: TypedEvent{
 					Type: JSAPILimitReachedAdvisoryType,
@@ -911,7 +913,7 @@ retry:
 		// then something is wrong for us to be both over the limit but unable to pull entries, so
 		// throw everything away and hope we recover from it.
 		s.rateLimitFormatWarnf("JetStream API queue limit reached, dropping %d requests", pending)
-		s.jsAPIRoutedReqs.drain()
+		atomic.AddInt64(&js.apiInflight, -int64(s.jsAPIRoutedReqs.drain()))
 
 		s.publishAdvisory(nil, JSAdvisoryAPILimitReached, JSAPILimitReachedAdvisory{
 			TypedEvent: TypedEvent{
@@ -923,8 +925,6 @@ retry:
 			Domain:  js.config.Domain,
 			Dropped: int64(pending),
 		})
-	} else {
-		atomic.StoreInt64(&js.apiInflight, int64(pending))
 	}
 }
 
diff --git a/server/raft.go b/server/raft.go
index c1102937bf..5ab37facfd 100644
--- a/server/raft.go
+++ b/server/raft.go
@@ -1962,7 +1962,7 @@ runner:
 	// just will remove them from the central monitoring map
 	queues := []interface {
 		unregister()
-		drain()
+		drain() int
 	}{n.reqs, n.votes, n.prop, n.entry, n.resp, n.apply}
 	for _, q := range queues {
 		q.drain()