diff --git a/pkg/app_watcher/appwatcher.go b/pkg/app_watcher/appwatcher.go
index a4fe66da..67ba6aa3 100644
--- a/pkg/app_watcher/appwatcher.go
+++ b/pkg/app_watcher/appwatcher.go
@@ -87,9 +87,8 @@ func (ctrl *ApplicationWatcher) onApplicationUpdated(old, new interface{}) {
 	if err != nil {
 		log.Warn().Err(err).Msg("appwatcher: could not get key for updated application")
 	}
-	// TODO
-	// have any of the Source repoURLs changed?
 	log.Trace().Str("key", key).Msg("appwatcher: onApplicationUpdated")
+	ctrl.cfg.VcsToArgoMap.UpdateApp(old.(appv1alpha1.Application), new.(appv1alpha1.Application))
 }
 
 func (ctrl *ApplicationWatcher) onApplicationDeleted(obj interface{}) {
@@ -102,6 +101,7 @@ func (ctrl *ApplicationWatcher) onApplicationDeleted(obj interface{}) {
 	}
 
 	log.Trace().Str("key", key).Msg("appwatcher: onApplicationDeleted")
+	ctrl.cfg.VcsToArgoMap.DeleteApp(obj.(appv1alpha1.Application))
 }
 
 /*
diff --git a/pkg/config/app_directory.go b/pkg/config/app_directory.go
index 603e6fe5..958056d4 100644
--- a/pkg/config/app_directory.go
+++ b/pkg/config/app_directory.go
@@ -163,6 +163,30 @@ func (d *AppDirectory) AddFile(appName, path string) {
 	d.appFiles[path] = append(d.appFiles[path], appName)
 }
 
+func (d *AppDirectory) RemoveApp(app v1alpha1.Application) {
+	// remove app from appsMap
+	delete(d.appsMap, app.Name)
+
+	// Clean up app from appDirs
+	sourcePath := getSourcePath(app)
+	d.appDirs[sourcePath] = removeFromSlice[string](d.appDirs[sourcePath], app.Name, func(a, b string) bool { return a == b })
+
+	// Clean up app from appFiles
+	src := app.Spec.GetSource()
+	srcPath := src.Path
+	if helm := src.Helm; helm != nil {
+		for _, param := range helm.FileParameters {
+			path := filepath.Join(srcPath, param.Path)
+			d.appFiles[path] = removeFromSlice[string](d.appFiles[path], app.Name, func(a, b string) bool { return a == b })
+		}
+
+		for _, valueFilePath := range helm.ValueFiles {
+			path := filepath.Join(srcPath, valueFilePath)
+			d.appFiles[path] = removeFromSlice[string](d.appFiles[path], app.Name, func(a, b string) bool { return a == b })
+		}
+	}
+}
+
 func mergeMaps[T any](first map[string]T, second map[string]T, combine func(T, T) T) map[string]T {
 	result := make(map[string]T)
 	for key, value := range first {
@@ -186,3 +210,12 @@ func mergeLists[T any](a []T, b []T) []T {
 func takeFirst[T any](a, _ T) T {
 	return a
 }
+
+func removeFromSlice[T any](slice []T, element T, equal func(T, T) bool) []T {
+	for i, j := range slice {
+		if equal(j, element) {
+			return append(slice[:i], slice[i+1:]...)
+		}
+	}
+	return slice
+}
diff --git a/pkg/config/config.go b/pkg/config/config.go
index cebfe480..54ed7326 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -53,6 +53,29 @@ func (v2a *VcsToArgoMap) AddApp(app v1alpha1.Application) {
 	appDirectory.ProcessApp(app)
 }
 
+func (v2a *VcsToArgoMap) UpdateApp(old v1alpha1.Application, new v1alpha1.Application) {
+	if new.Spec.Source == nil {
+		log.Warn().Msgf("%s/%s: no source, skipping", new.Namespace, new.Name)
+		return
+	}
+
+	oldAppDirectory := v2a.GetAppsInRepo(old.Spec.Source.RepoURL)
+	oldAppDirectory.RemoveApp(old)
+
+	newAppDirectory := v2a.GetAppsInRepo(new.Spec.Source.RepoURL)
+	newAppDirectory.ProcessApp(new)
+}
+
+func (v2a *VcsToArgoMap) DeleteApp(app v1alpha1.Application) {
+	if app.Spec.Source == nil {
+		log.Warn().Msgf("%s/%s: no source, skipping", app.Namespace, app.Name)
+		return
+	}
+
+	oldAppDirectory := v2a.GetAppsInRepo(app.Spec.Source.RepoURL)
+	oldAppDirectory.RemoveApp(app)
+}
+
 type ServerConfig struct {
 	UrlPrefix     string
 	WebhookSecret string
diff --git a/pkg/server/server.go b/pkg/server/server.go
index fd2abe11..be35585b 100644
--- a/pkg/server/server.go
+++ b/pkg/server/server.go
@@ -15,6 +15,7 @@ import (
 	"github.com/spf13/viper"
 	"github.com/ziflex/lecho/v3"
 
+	"github.com/zapier/kubechecks/pkg/app_watcher"
 	"github.com/zapier/kubechecks/pkg/config"
 	"github.com/zapier/kubechecks/pkg/vcs"
 )
@@ -22,18 +23,33 @@ import (
 const KubeChecksHooksPathPrefix = "/hooks"
 
 type Server struct {
-	cfg *config.ServerConfig
+	cfg        *config.ServerConfig
+	appWatcher *app_watcher.ApplicationWatcher
 }
 
 func NewServer(cfg *config.ServerConfig) *Server {
-	return &Server{cfg: cfg}
+	var appWatcher *app_watcher.ApplicationWatcher
+	if viper.GetBool("monitor-all-applications") {
+		argoMap, err := config.BuildAppsMap(context.TODO())
+		if err != nil {
+			log.Fatal().Err(err).Msg("could not build VcsToArgoMap")
+		}
+		cfg.VcsToArgoMap = argoMap
+
+		appWatcher, err = app_watcher.NewApplicationWatcher(cfg)
+		if err != nil {
+			log.Fatal().Err(err).Msg("could not create ApplicationWatcher")
+		}
+	} else {
+		cfg.VcsToArgoMap = config.NewVcsToArgoMap()
+	}
+
+	return &Server{cfg: cfg, appWatcher: appWatcher}
 }
 
 func (s *Server) Start(ctx context.Context) {
-	if argoMap, err := s.buildVcsToArgoMap(ctx); err != nil {
-		log.Warn().Err(err).Msg("failed to build vcs app map from argo")
-	} else {
-		s.cfg.VcsToArgoMap = argoMap
+	if s.appWatcher != nil {
+		go s.appWatcher.Run(context.Background(), 1)
 	}
 
 	if err := s.ensureWebhooks(); err != nil {
@@ -120,13 +136,3 @@ func (s *Server) ensureWebhooks() error {
 
 	return nil
 }
-
-func (s *Server) buildVcsToArgoMap(ctx context.Context) (config.VcsToArgoMap, error) {
-	if !viper.GetBool("monitor-all-applications") {
-		return config.NewVcsToArgoMap(), nil
-	}
-
-	log.Debug().Msg("building VCS to Application Map")
-
-	return config.BuildAppsMap(ctx)
-}