diff --git a/v3/UNRELEASED_CHANGELOG.md b/v3/UNRELEASED_CHANGELOG.md
index 33638e7fc86..303e7c354fc 100644
--- a/v3/UNRELEASED_CHANGELOG.md
+++ b/v3/UNRELEASED_CHANGELOG.md
@@ -17,6 +17,7 @@ After processing, the content will be moved to the main changelog and this file
 
 ## Added
 <!-- New features, capabilities, or enhancements -->
+- Add `LinuxOptions.ApplicationID` to override the GTK application ID, which Flatpak and Snap require to be a domain the publisher controls (#6020)
 
 ## Changed
 <!-- Changes in existing functionality -->
diff --git a/v3/pkg/application/application_linux.go b/v3/pkg/application/application_linux.go
index 6ecd09c03f4..15adb80a41f 100644
--- a/v3/pkg/application/application_linux.go
+++ b/v3/pkg/application/application_linux.go
@@ -233,9 +233,16 @@ func (a *linuxApp) unregisterWindow(window windowPointer) {
 
 func newPlatformApp(parent *App) *linuxApp {
 	name := sanitizeAppName(parent.options.Name)
+	application := pointer(nil)
+	if id := parent.options.Linux.ApplicationID; id != "" {
+		application = appNewWithID(id)
+	}
+	if application == nil {
+		application = appNew(name)
+	}
 	app := &linuxApp{
 		parent:      parent,
-		application: appNew(name),
+		application: application,
 		activated:   make(chan struct{}),
 		windowMap:   map[windowPointer]uint{},
 	}
diff --git a/v3/pkg/application/application_options.go b/v3/pkg/application/application_options.go
index 560436a36d8..e13637e2b27 100644
--- a/v3/pkg/application/application_options.go
+++ b/v3/pkg/application/application_options.go
@@ -329,6 +329,16 @@ type LinuxOptions struct {
 	//
 	//[see the docs]: https://docs.gtk.org/glib/func.set_prgname.html
 	ProgramName string
+
+	// ApplicationID overrides the GTK application ID, which defaults to
+	// org.wails.<name>.
+	//
+	// It is the app ID a Wayland compositor sees, and a desktop entry is found
+	// by matching it, so a window's icon and its grouping both hang off it.
+	// Flatpak and Snap go further and require the ID to be a domain the
+	// publisher controls, which the default cannot be. Must be a valid GTK
+	// application ID; an invalid one is ignored in favour of the default.
+	ApplicationID string
 }
 
 /********* iOS Options *********/
diff --git a/v3/pkg/application/linux_cgo.go b/v3/pkg/application/linux_cgo.go
index e4751c88262..67d3d96ce18 100644
--- a/v3/pkg/application/linux_cgo.go
+++ b/v3/pkg/application/linux_cgo.go
@@ -144,12 +144,29 @@ func appName() string {
 }
 
 func appNew(name string) pointer {
+	// A GApplication ID is capped at 255 characters and the prefix takes ten,
+	// so a long enough app name would otherwise build an ID GTK refuses,
+	// leaving no application at all.
+	const maxNameLength = 245
+	if len(name) > maxNameLength {
+		name = name[:maxNameLength]
+	}
+	return appNewWithID(fmt.Sprintf("org.wails.%s", name))
+}
+
+// appNewWithID creates the GtkApplication under an explicit ID. GTK refuses an
+// invalid one, so it is checked first and the caller's default used instead —
+// an application that fails to construct has no window to report the problem
+// in.
+func appNewWithID(appID string) pointer {
 	C.install_signal_handlers()
 
-	appId := fmt.Sprintf("org.wails.%s", name)
-	nameC := C.CString(appId)
-	defer C.free(unsafe.Pointer(nameC))
-	return pointer(C.gtk_application_new(nameC, C.APPLICATION_DEFAULT_FLAGS))
+	idC := C.CString(appID)
+	defer C.free(unsafe.Pointer(idC))
+	if C.g_application_id_is_valid(idC) == 0 {
+		return nil
+	}
+	return pointer(C.gtk_application_new(idC, C.APPLICATION_DEFAULT_FLAGS))
 }
 
 func setProgramName(prgName string) {