diff --git a/crates/pacdef_core/src/backend/actual/flatpak.rs b/crates/pacdef_core/src/backend/actual/flatpak.rs
index 100f595..e3dc6c3 100644
--- a/crates/pacdef_core/src/backend/actual/flatpak.rs
+++ b/crates/pacdef_core/src/backend/actual/flatpak.rs
@@ -27,12 +27,20 @@ const SUPPORTS_AS_DEPENDENCY: bool = false;
 impl Backend for Flatpak {
     impl_backend_constants!();
 
+    fn get_switches_runtime(&self) -> Switches {
+        if self.systemwide {
+            &[]
+        } else {
+            &["--user"]
+        }
+    }
+
     fn get_all_installed_packages(&self) -> Result<HashSet<Package>> {
-        Flatpak::get_installed_packages(true)
+        self.get_installed_packages(true)
     }
 
     fn get_explicitly_installed_packages(&self) -> Result<HashSet<Package>> {
-        Flatpak::get_installed_packages(false)
+        self.get_installed_packages(false)
     }
 
     fn make_dependency(&self, _: &[Package]) -> Result<ExitStatus> {
@@ -48,12 +56,15 @@ impl Flatpak {
         }
     }
 
-    fn get_installed_packages(include_implicit: bool) -> Result<HashSet<Package>> {
+    fn get_installed_packages(&self, include_implicit: bool) -> Result<HashSet<Package>> {
         let mut cmd = Command::new(BINARY);
         cmd.args(&["list", "--columns=application"]);
         if !include_implicit {
             cmd.arg("--app");
         }
+        if !self.systemwide {
+            cmd.arg("--user");
+        }
 
         let output = String::from_utf8(cmd.output()?.stdout)?;
         Ok(
diff --git a/crates/pacdef_core/src/backend/backend_trait.rs b/crates/pacdef_core/src/backend/backend_trait.rs
index 8e6be52..9b84448 100644
--- a/crates/pacdef_core/src/backend/backend_trait.rs
+++ b/crates/pacdef_core/src/backend/backend_trait.rs
@@ -49,6 +49,11 @@ pub trait Backend: Debug {
     /// [`Backend::supports_as_dependency`].
     fn get_switches_make_dependency(&self) -> Switches;
 
+    /// Get CLI switches evaluated at runtime
+    fn get_switches_runtime(&self) -> Switches {
+        &[]
+    }
+
     /// Load all packages from a set of groups. The backend will visit all groups,
     /// find its own section, and clone all packages into its own struct.
     fn load(&mut self, groups: &HashSet<Group>);
@@ -80,6 +85,7 @@ pub trait Backend: Debug {
     fn install_packages(&self, packages: &[Package], noconfirm: bool) -> Result<ExitStatus> {
         let mut cmd = Command::new(self.get_binary());
         cmd.args(self.get_switches_install());
+        cmd.args(self.get_switches_runtime());
 
         if noconfirm {
             cmd.args(self.get_switches_noconfirm());
@@ -102,6 +108,7 @@ pub trait Backend: Debug {
     fn make_dependency(&self, packages: &[Package]) -> Result<ExitStatus> {
         let mut cmd = Command::new(self.get_binary());
         cmd.args(self.get_switches_make_dependency());
+        cmd.args(self.get_switches_runtime());
 
         for p in packages {
             cmd.arg(format!("{p}"));
@@ -115,6 +122,7 @@ pub trait Backend: Debug {
     fn remove_packages(&self, packages: &[Package], noconfirm: bool) -> Result<ExitStatus> {
         let mut cmd = Command::new(self.get_binary());
         cmd.args(self.get_switches_remove());
+        cmd.args(self.get_switches_runtime());
 
         if noconfirm {
             cmd.args(self.get_switches_noconfirm());
@@ -143,6 +151,7 @@ pub trait Backend: Debug {
     fn show_package_info(&self, package: &Package) -> Result<ExitStatus> {
         let mut cmd = Command::new(self.get_binary());
         cmd.args(self.get_switches_info());
+        cmd.args(self.get_switches_runtime());
         cmd.arg(format!("{package}"));
         cmd.status()
             .with_context(|| format!("running command {cmd:?}"))