diff --git a/crates/pacdef_core/src/backend/actual/flatpak.rs b/crates/pacdef_core/src/backend/actual/flatpak.rs
index af284db..43a275c 100644
--- a/crates/pacdef_core/src/backend/actual/flatpak.rs
+++ b/crates/pacdef_core/src/backend/actual/flatpak.rs
@@ -10,6 +10,7 @@ use crate::{impl_backend_constants, Group, Package};
 #[derive(Debug, Clone)]
 pub struct Flatpak {
     pub(crate) packages: HashSet<Package>,
+    pub(crate) systemwide: bool,
 }
 
 const BINARY: Text = "flatpak";
@@ -26,12 +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> {
@@ -43,15 +52,19 @@ impl Flatpak {
     pub(crate) fn new() -> Self {
         Self {
             packages: HashSet::new(),
+            systemwide: true,
         }
     }
 
-    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:?}"))
diff --git a/crates/pacdef_core/src/config.rs b/crates/pacdef_core/src/config.rs
index e0e39f8..d791425 100644
--- a/crates/pacdef_core/src/config.rs
+++ b/crates/pacdef_core/src/config.rs
@@ -13,6 +13,8 @@ pub struct Config {
     pub aur_helper: String,
     /// Additional arguments to pass to `aur_helper` when removing a package.
     pub aur_rm_args: Option<Vec<String>>,
+    /// Install Flatpak packages system-wide
+    pub flatpak_systemwide: bool,
     /// Warn the user when a group is not a symlink.
     pub warn_not_symlinks: bool,
     /// Backends the user does not want to use even though the binary exists.
@@ -68,6 +70,7 @@ impl Default for Config {
         Self {
             aur_helper: "paru".into(),
             aur_rm_args: None,
+            flatpak_systemwide: true,
             warn_not_symlinks: true,
             disabled_backends: vec![],
         }
diff --git a/crates/pacdef_core/src/core.rs b/crates/pacdef_core/src/core.rs
index 7a1cb67..dcda504 100644
--- a/crates/pacdef_core/src/core.rs
+++ b/crates/pacdef_core/src/core.rs
@@ -128,6 +128,13 @@ impl Pacdef {
                 arch.aur_rm_args = self.config.aur_rm_args.take();
             }
         }
+
+        #[cfg(feature = "flatpak")]
+        {
+            if let Some(flatpak) = backend.as_any_mut().downcast_mut::<crate::backend::Flatpak>() {
+                flatpak.systemwide = self.config.flatpak_systemwide;
+            }
+        }
     }
 
     fn install_packages(&mut self, args: &ArgMatches) -> Result<()> {