diff --git a/crates/core/tedge_agent/src/operation_workflows/persist.rs b/crates/core/tedge_agent/src/operation_workflows/persist.rs
index 01d13efbc9..836e400078 100644
--- a/crates/core/tedge_agent/src/operation_workflows/persist.rs
+++ b/crates/core/tedge_agent/src/operation_workflows/persist.rs
@@ -3,7 +3,6 @@ use camino::Utf8Path;
 use camino::Utf8PathBuf;
 use log::error;
 use std::collections::HashMap;
-use std::collections::HashSet;
 use tedge_api::mqtt_topics::EntityTopicId;
 use tedge_api::mqtt_topics::MqttSchema;
 use tedge_api::mqtt_topics::OperationType;
@@ -41,10 +40,8 @@ pub struct WorkflowRepository {
     // Map each user defined workflow to its version and workflow file
     definitions: HashMap<OperationName, (WorkflowVersion, Utf8PathBuf)>,
 
-    // Set of workflow in-use
-    //
-    // TODO Implement the cleanup logic
-    in_use_copies: HashSet<WorkflowVersion>,
+    // Map each workflow version to the count of instance using it
+    in_use_copies: HashMap<WorkflowVersion, u32>,
 
     // The in-memory representation of all the workflows (builtin, user-defined, in-use).
     workflows: WorkflowSupervisor,
@@ -59,7 +56,7 @@ impl WorkflowRepository {
         let workflows = WorkflowSupervisor::default();
         let state_dir = state_dir.join("workflows-in-use");
         let definitions = HashMap::new();
-        let in_use_copies = HashSet::new();
+        let in_use_copies = HashMap::new();
         Self {
             builtin_workflows,
             custom_workflows_dir,
@@ -138,7 +135,10 @@ impl WorkflowRepository {
                 WorkflowSource::UserDefined(version)
             }
             WorkflowSource::InUseCopy(_) => {
-                self.in_use_copies.insert(version.clone());
+                self.in_use_copies
+                    .entry(version.clone())
+                    .and_modify(|count| *count += 1)
+                    .or_insert(1);
                 WorkflowSource::InUseCopy(version)
             }
             WorkflowSource::BuiltIn => WorkflowSource::BuiltIn,
@@ -265,19 +265,26 @@ impl WorkflowRepository {
         operation: &OperationName,
         version: &WorkflowVersion,
     ) {
-        if self.in_use_copies.contains(version) {
+        if let Some(count) = self.in_use_copies.get_mut(version) {
+            *count += 1;
             return;
         };
+
         if let Some((_, source)) = self.definitions.get(operation) {
-            let target = self.state_dir.join(version).with_extension("toml");
+            let target = self.workflow_copy_path(operation, version);
             if let Err(err) = tokio::fs::copy(source.clone(), target.clone()).await {
                 error!("Fail to persist a copy of {source} as {target}: {err}");
             } else {
-                self.in_use_copies.insert(version.clone());
+                self.in_use_copies.insert(version.clone(), 1);
             }
         }
     }
 
+    fn workflow_copy_path(&self, operation: &OperationName, version: &WorkflowVersion) -> Utf8PathBuf {
+        let filename = format!("{operation}-{version}");
+        self.state_dir.join(filename).with_extension("toml")
+    }
+
     async fn load_latest_version(&mut self, operation: &OperationName) {
         if let Some((path, version, workflow)) = self.get_latest_version(operation).await {
             if let Err(err) = self.load_operation_workflow(
@@ -290,6 +297,22 @@ impl WorkflowRepository {
         }
     }
 
+    async fn release_in_use_copy(&mut self, operation: &OperationName, version: &WorkflowVersion) {
+        if let Some(count) = self.in_use_copies.get_mut(version) {
+            *count -= 1;
+            if *count == 0 {
+                return;
+            }
+        }
+
+        self.in_use_copies.remove(version);
+
+        let target = self.workflow_copy_path(operation, version);
+        if let Err(err) = tokio::fs::remove_file(target.clone()).await {
+            error!("Fail to remove the workflow copy at {target}: {err}");
+        }
+    }
+
     async fn get_latest_version(
         &mut self,
         operation: &OperationName,
@@ -361,6 +384,11 @@ impl WorkflowRepository {
         if command_state.is_init() {
             // A new command instance must use the latest on-disk version of the operation workflow
             self.load_latest_version(&operation.to_string()).await;
+        } else if command_state.is_finished() {
+            // Clear the cache if this happens to be the latest instance using that version of the workflow
+            if let Some(version) = command_state.workflow_version() {
+                self.release_in_use_copy(&operation.to_string(), &version).await;
+            }
         }
 
         match self
diff --git a/crates/core/tedge_api/src/workflow/supervisor.rs b/crates/core/tedge_api/src/workflow/supervisor.rs
index 7f19536e93..00d2fa4be0 100644
--- a/crates/core/tedge_api/src/workflow/supervisor.rs
+++ b/crates/core/tedge_api/src/workflow/supervisor.rs
@@ -56,7 +56,7 @@ impl WorkflowSupervisor {
             versions.remove(version);
         }
 
-        let (empty,builtin_restored) = match self.workflows.get(&operation) {
+        let (empty, builtin_restored) = match self.workflows.get(&operation) {
             None => (true, false),
             Some(version) if version.is_empty() => (true, false),
             Some(version) if version.is_builtin() => (false, true),