diff --git a/src/liteclient.cc b/src/liteclient.cc
index 82573e97..21a8acf6 100644
--- a/src/liteclient.cc
+++ b/src/liteclient.cc
@@ -757,7 +757,7 @@ bool LiteClient::isTargetActive(const Uptane::Target& target) const {
   return target.filename() == current.filename() && target.sha256Hash() == current.sha256Hash();
 }
 
-bool LiteClient::appsInSync(const Uptane::Target& target) const {
+bool LiteClient::appsInSync(const Uptane::Target& target, bool cleanup_removed_apps) const {
   if (package_manager_->name() == ComposeAppManager::Name) {
     auto* compose_pacman = dynamic_cast<ComposeAppManager*>(package_manager_.get());
     if (compose_pacman == nullptr) {
@@ -766,7 +766,7 @@ bool LiteClient::appsInSync(const Uptane::Target& target) const {
     }
     LOG_INFO << "Checking Active Target status...";
     auto no_any_app_to_update = compose_pacman->checkForAppsToUpdate(target);
-    if (no_any_app_to_update) {
+    if (cleanup_removed_apps && no_any_app_to_update) {
       compose_pacman->handleRemovedApps(getCurrent());
     }
 
diff --git a/src/liteclient.h b/src/liteclient.h
index 77362fb7..7ed7abf5 100644
--- a/src/liteclient.h
+++ b/src/liteclient.h
@@ -67,7 +67,7 @@ class LiteClient {
   void reportHwInfo();
   void reportAppsState();
   bool isTargetActive(const Uptane::Target& target) const;
-  bool appsInSync(const Uptane::Target& target) const;
+  bool appsInSync(const Uptane::Target& target, bool cleanup_removed_apps = true) const;
   void setAppsNotChecked();
   std::string getDeviceID() const;
   static void update_request_headers(std::shared_ptr<HttpClient>& http_client, const Uptane::Target& target,
diff --git a/src/main.cc b/src/main.cc
index ac282e19..e49887b2 100644
--- a/src/main.cc
+++ b/src/main.cc
@@ -259,6 +259,7 @@ static int daemon_main(LiteClient& client, const bpo::variables_map& variables_m
     std::string cor_id;
     storage::Volume::UsageInfo stat;
   } state_when_download_failed{Hash{"", ""}, "", {.err = "undefined"}};
+  bool cleanup_removed_apps = true;
 
   while (true) {
     LOG_INFO << "Active Target: " << current.filename() << ", sha256: " << current.sha256Hash();
@@ -399,7 +400,7 @@ static int daemon_main(LiteClient& client, const bpo::variables_map& variables_m
                    << " Skipping its installation.";
         }
         data::ResultCode::Numeric rc{data::ResultCode::Numeric::kOk};
-        if (!client.appsInSync(current)) {
+        if (!client.appsInSync(current, cleanup_removed_apps)) {
           client.checkForUpdatesEnd(target_to_install);
           rc = do_app_sync(client);
           if (rc == data::ResultCode::Numeric::kOk) {
@@ -411,6 +412,8 @@ static int daemon_main(LiteClient& client, const bpo::variables_map& variables_m
           LOG_INFO << "Device is up-to-date";
           client.checkForUpdatesEnd(Uptane::Target::Unknown());
         }
+        // Automatically cleanup during check only once. A cleanup will also occur after a new target is installed
+        cleanup_removed_apps = false;
       }
 
     } catch (const std::exception& exc) {