diff --git a/packages/node_modules/@node-red/runtime/lib/flows/Flow.js b/packages/node_modules/@node-red/runtime/lib/flows/Flow.js
index d98940a41..2a9b82c2a 100644
--- a/packages/node_modules/@node-red/runtime/lib/flows/Flow.js
+++ b/packages/node_modules/@node-red/runtime/lib/flows/Flow.js
@@ -74,12 +74,16 @@ class Flow {
         // Graceful Shutdown props
         /** @type {Number} */
         this.pendingMsgCount = 0;
+        /** @type {Record<string, number>} */
+        this.msgInProgressNodeMap = {};
         /** @type {object[]|null} */
         this.shutdownScope = null;
         /** @type {Number} */
         this.shutdownTimeout = 10000; // 10s
         /** @type {object[]} */
         this.messageInitiatorNodes = [];
+        /** @type {Record<string, string[]>} */
+        this.wiredNodeMap = {};
     }
 
     /**
@@ -150,14 +154,37 @@ class Flow {
         this.parent.log(msg);
     }
 
-    decrementPendindMsgCount() {
+    /**
+     * This method is called when a node finishes processing a message.
+     * e.g. `node.done()` or `node.done(error)`.
+     * @param {object} node
+     */
+    decrementPendingMsgCount(node) {
         this.pendingMsgCount--;
-        this.debug("Decrement pending messages count to: " + this.pendingMsgCount);
+        if (this.msgInProgressNodeMap.hasOwnProperty(node.id)) {
+            this.msgInProgressNodeMap[node.id]--;
+            if (this.msgInProgressNodeMap[node.id] <= 0) {
+                delete this.msgInProgressNodeMap[node.id];
+            }
+        }
+        this.trace("decrement pending messages count to: " + this.pendingMsgCount);
+        this.trace(`decrement in-progress msg to: ${this.msgInProgressNodeMap[node.id] || 0} for: ${node.id}`);
     }
 
-    incrementPendingMsgCount() {
+    /**
+     * This method is called when a node sends a message.
+     * e.g. `node.send(msg)` or `node.receive(msg)`.
+     * @param {object} node
+     */
+    incrementPendingMsgCount(node) {
         this.pendingMsgCount++;
-        this.debug("Increment pending messages count to: " + this.pendingMsgCount);
+        if (this.msgInProgressNodeMap[node.id]) {
+            this.msgInProgressNodeMap[node.id]++;
+        } else {
+            this.msgInProgressNodeMap[node.id] = 1;
+        }
+        this.trace("increment pending messages count to: " + this.pendingMsgCount);
+        this.trace(`increment in-progress msg to: ${this.msgInProgressNodeMap[node.id]} for: ${node.id}`);
     }
 
     /**
@@ -280,6 +307,7 @@ class Flow {
             }
         }
 
+        this.wiredNodeMap = {};
         for (id in this.flow.nodes) {
             if (this.flow.nodes.hasOwnProperty(id)) {
                 node = this.flow.nodes[id];
@@ -321,6 +349,15 @@ class Flow {
                             }
                         }
                     }
+                    if (node.wires) {
+                        // Create a map with incoming wires for each node
+                        node.wires.forEach((output) => {
+                            output.forEach((wire) => {
+                                this.wiredNodeMap[wire] = this.wiredNodeMap[wire] || [];
+                                this.wiredNodeMap[wire].push(node.id);
+                            });
+                        });
+                    }
                 } else {
                     this.debug("not starting disabled node : "+id);
                 }
@@ -383,7 +420,9 @@ class Flow {
      */
     stop(stopList, removedList) {
         this.trace("stop "+this.TYPE);
+        let fullStop = false;
         if (!stopList) {
+            fullStop = true;
             stopList = Object.keys(this.activeNodes);
         }
         // this.trace(" stopList: "+stopList.join(","))
@@ -425,29 +464,63 @@ class Flow {
                 }
             }
 
+            /** @type {Set<string>} */
+            const lookupNodes = new Set();
+
+            if (!fullStop) {
+                // Create a list of nodes wired upstream of nodes to be stopped.
+                const list = stopList.slice();
+                while (list.length) {
+                    const id = list.pop();
+                    if (lookupNodes.has(id)) {
+                        continue;
+                    }
+                    lookupNodes.add(id);
+                    if (this.wiredNodeMap[id]) {
+                        list.push(...this.wiredNodeMap[id]);
+                    }
+                }
+            }
+
             shutdownPromise = new Promise((resolve, _reject) => {
                 let remainingPeriod = this.shutdownTimeout;
                 const loop = () => {
-                    this.debug(`Pending message count: ${this.pendingMsgCount}`);
-                    if (this.shutdownScope === null) {
-                        if (this.pendingMsgCount === 0) {
-                            this.pendingMsgCount = 0;
-                            return resolve();
-                        }
-                    } else if (this.shutdownScope.length) {
-                        let count = 0;
-                        this.shutdownScope.forEach((flow) => {
-                            if (flow && "pendingMsgCount" in flow) {
-                                count += flow.pendingMsgCount;
+                    if (fullStop) {
+                        this.debug(`Pending message count: ${this.pendingMsgCount}`);
+                        if (this.shutdownScope === null) {
+                            if (this.pendingMsgCount === 0) {
+                                return resolve();
                             }
-                        });
-                        if (count === 0) {
-                            this.pendingMsgCount = 0;
+                        } else if (this.shutdownScope.length) {
+                            let count = 0;
+                            this.shutdownScope.forEach((flow) => {
+                                if (flow instanceof Flow) {
+                                    count += flow.pendingMsgCount;
+                                }
+                            });
+                            if (count === 0) {
+                                return resolve();
+                            }
+                        }
+                        if (remainingPeriod < 0) {
+                            this.error("Timeout for graceful shutdown has expired");
+                            return resolve();
+                        }
+                    } else {
+                        let inProgress = false;
+                        for (const id of Object.keys(this.msgInProgressNodeMap)) {
+                            if (lookupNodes.has(id)) {
+                                inProgress = true;
+                                break;
+                            }
+                        }
+                        if (!inProgress) {
+                            return resolve();
+                        }
+                        if (remainingPeriod < 0) {
+                            this.error("Timeout for graceful shutdown has expired");
                             return resolve();
                         }
-                    } else if (remainingPeriod < 0) {
-                        this.pendingMsgCount = 0;
-                        return resolve();
                     }
                     remainingPeriod -= 1000;
                     setTimeout(loop, 1000); // polling every 1000ms
@@ -914,7 +987,7 @@ function handlePreDeliver(flow,sendEvent, reportError) {
         } else if (err !== false) {
             // node.send(msg) called
             // Do it now to avoid next loop and an offbeat count
-            flow.incrementPendingMsgCount();
+            flow.incrementPendingMsgCount(sendEvent.destination.node);
             if (asyncMessageDelivery) {
                 setImmediate(function() {
                     deliverMessageToDestination(sendEvent)
diff --git a/packages/node_modules/@node-red/runtime/lib/nodes/Node.js b/packages/node_modules/@node-red/runtime/lib/nodes/Node.js
index 5ccfaa8e5..db3e90fe3 100644
--- a/packages/node_modules/@node-red/runtime/lib/nodes/Node.js
+++ b/packages/node_modules/@node-red/runtime/lib/nodes/Node.js
@@ -133,7 +133,7 @@ Node.prototype._complete = function(msg,error) {
     this.metric("done",msg);
     if (this._flow) {
         // done() or done(error) called
-        this._flow.decrementPendindMsgCount();
+        this._flow.decrementPendingMsgCount(this);
     }
     hooks.trigger("onComplete",{ msg: msg, error: error, node: { id: this.id, node: this }}, err => {
         if (err) {
@@ -513,7 +513,7 @@ Node.prototype._receive = function (msg) {
 Node.prototype.receive = function (msg) {
     if (this._flow) {
         // Equivalent to node.send(msg) without handleOnSend
-        this._flow.incrementPendingMsgCount();
+        this._flow.incrementPendingMsgCount(this);
     }
     this._receive(msg);
 };