diff --git a/files/etc/ublue-update.d/system/00-system-update.py b/files/etc/ublue-update.d/system/00-system-rebase.py
similarity index 90%
rename from files/etc/ublue-update.d/system/00-system-update.py
rename to files/etc/ublue-update.d/system/00-system-rebase.py
index eb3e399..412024c 100755
--- a/files/etc/ublue-update.d/system/00-system-update.py
+++ b/files/etc/ublue-update.d/system/00-system-rebase.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 from subprocess import run
 from json import loads, load
@@ -106,11 +106,3 @@ def check_for_rebase():
         else:
             print("rebase failed!, command output:")
             print(rebase_out.stdout.decode("utf-8"))
-    update_cmd = ["rpm-ostree", "upgrade"]
-    update_out = run(update_cmd, capture_output=True)
-    if update_out.returncode != 0:
-        print(
-            f"rpm-ostree upgrade returned code {update_out.returncode}, program output:"
-        )
-        print(update_out.stdout.decode("utf-8"))
-        os._exit(update_out.returncode)
diff --git a/files/etc/ublue-update.d/system/01-flatpak-system-update.sh b/files/etc/ublue-update.d/system/01-flatpak-system-update.sh
deleted file mode 100755
index cba7208..0000000
--- a/files/etc/ublue-update.d/system/01-flatpak-system-update.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-/usr/bin/flatpak --system update -y --noninteractive
diff --git a/files/etc/ublue-update.d/system/01-topgrade.sh b/files/etc/ublue-update.d/system/01-topgrade.sh
new file mode 100755
index 0000000..5e25f68
--- /dev/null
+++ b/files/etc/ublue-update.d/system/01-topgrade.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/bash
+
+/usr/bin/topgrade --config /etc/ublue-update/topgrade-system.toml
diff --git a/files/etc/ublue-update.d/system/02-flatpak-system-repair-cleanup.sh b/files/etc/ublue-update.d/system/02-flatpak-system-repair-cleanup.sh
deleted file mode 100755
index b10acc8..0000000
--- a/files/etc/ublue-update.d/system/02-flatpak-system-repair-cleanup.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-/usr/bin/flatpak uninstall --system --unused -y --noninteractive
-/usr/bin/flatpak repair --system
diff --git a/files/etc/ublue-update.d/user/00-flatpak-user-update.sh b/files/etc/ublue-update.d/user/00-flatpak-user-update.sh
deleted file mode 100755
index 76d3b79..0000000
--- a/files/etc/ublue-update.d/user/00-flatpak-user-update.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-/usr/bin/flatpak --user update -y --noninteractive
diff --git a/files/etc/ublue-update.d/user/01-flatpak-user-repair-cleanup.sh b/files/etc/ublue-update.d/user/01-flatpak-user-repair-cleanup.sh
deleted file mode 100755
index 8046e76..0000000
--- a/files/etc/ublue-update.d/user/01-flatpak-user-repair-cleanup.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-
-
-/usr/bin/flatpak uninstall --user --unused -y --noninteractive
-/usr/bin/flatpak repair --user
diff --git a/files/etc/ublue-update.d/user/02-distrobox-user-update.sh b/files/etc/ublue-update.d/user/02-distrobox-user-update.sh
deleted file mode 100755
index a45075b..0000000
--- a/files/etc/ublue-update.d/user/02-distrobox-user-update.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-
-if [ -x /usr/bin/distrobox ]; then
-    unset SUDO_USER # avoid distrobox sudo checks
-    /usr/bin/distrobox upgrade -a
-fi
diff --git a/files/etc/ublue-update.d/user/03-fleek-user-update.sh b/files/etc/ublue-update.d/user/03-fleek-user-update.sh
deleted file mode 100755
index c322993..0000000
--- a/files/etc/ublue-update.d/user/03-fleek-user-update.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-
-if [ -x /var/usrlocal/bin/fleek ]; then
-    /var/usrlocal/bin/fleek update -a
-fi
diff --git a/files/etc/ublue-update.d/user/04-brew-update.sh b/files/etc/ublue-update.d/user/04-brew-update.sh
deleted file mode 100644
index cb61d0f..0000000
--- a/files/etc/ublue-update.d/user/04-brew-update.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-
-if command -v /var/home/linuxbrew/.linuxbrew/bin/brew; then
-	/var/home/linuxbrew/.linuxbrew/bin/brew update --auto-update
-fi
diff --git a/files/usr/etc/ublue-update/topgrade-system.toml b/files/usr/etc/ublue-update/topgrade-system.toml
new file mode 100644
index 0000000..9c74827
--- /dev/null
+++ b/files/usr/etc/ublue-update/topgrade-system.toml
@@ -0,0 +1,10 @@
+[misc]
+only = ["system", "flatpak"]
+ignore_failures = ["flatpak"]
+skip_notify = true
+assume_yes = true
+no_retry = true
+no_self_update = true
+
+[linux]
+rpm_ostree = true
diff --git a/files/usr/etc/ublue-update/topgrade-user.toml b/files/usr/etc/ublue-update/topgrade-user.toml
new file mode 100644
index 0000000..a83ac17
--- /dev/null
+++ b/files/usr/etc/ublue-update/topgrade-user.toml
@@ -0,0 +1,13 @@
+[misc]
+only = ["flatpak", "distrobox"]
+ignore_failures = ["flatpak", "distrobox"]
+skip_notify = true
+assume_yes = true
+no_retry = true
+no_self_update = true
+
+[distrobox]
+use_root = false
+
+[flatpak]
+use_sudo = false
diff --git a/src/ublue_update/cli.py b/src/ublue_update/cli.py
index a8e501e..b03af9b 100644
--- a/src/ublue_update/cli.py
+++ b/src/ublue_update/cli.py
@@ -160,8 +160,8 @@ def run_updates(system, system_update_available):
                     "DISPLAY=:0",
                     f"XDG_RUNTIME_DIR={xdg_runtime_dir}",
                     f"DBUS_SESSION_BUS_ADDRESS=unix:path={xdg_runtime_dir}/bus",
-                    "/usr/bin/ublue-update",
-                    "-f",
+                    "/usr/bin/topgrade",
+                    "--config /etc/ublue-update/topgrade-user.toml",
                 ],
                 capture_output=True,
             )
@@ -181,7 +181,6 @@ def run_updates(system, system_update_available):
             raise Exception(
                 "ublue-update needs to be run as root to perform system updates!"
             )
-        run_update_scripts(f"{root_dir}/user/")
     release_lock(fd)
     os._exit(0)
 
diff --git a/ublue-update.spec b/ublue-update.spec
index 1717145..0ae4e2f 100644
--- a/ublue-update.spec
+++ b/ublue-update.spec
@@ -45,7 +45,6 @@ ls
 ls src
 black src
 flake8 src
-shellcheck files/etc/%{NAME}.d/user/*.sh
 shellcheck files/etc/%{NAME}.d/system/*.sh
 black files/etc/%{NAME}.d/system/*.py
 flake8 files/etc/%{NAME}.d/system/*.py
@@ -56,6 +55,13 @@ flake8 files/etc/%{NAME}.d/system/*.py
 %pyproject_save_files ublue_update
 cp -rp files/etc files/usr %{buildroot}
 
+%pre
+if [ ! -x /usr/bin/topgrade ]
+then
+    echo "Topgrade not installed. Please install Topgrade (https://github.com/topgrade-rs/topgrade) to use %{name}."
+    exit 1
+fi
+
 %post
 %systemd_post %{NAME}.timer
 
@@ -67,8 +73,7 @@ cp -rp files/etc files/usr %{buildroot}
 %attr(0644,root,root) %{_exec_prefix}/lib/systemd/system/%{NAME}.service
 %attr(0644,root,root) %{_exec_prefix}/lib/systemd/system/%{NAME}.timer
 %attr(0644,root,root) %{_exec_prefix}/lib/systemd/system-preset/00-%{NAME}.preset
-%attr(0644,root,root) %{_exec_prefix}/etc/%{NAME}/%{NAME}.toml
-%attr(0755,root,root) %{_sysconfdir}/%{NAME}.d/user/*
+%attr(0644,root,root) %{_exec_prefix}/etc/%{NAME}/*.toml
 %attr(0755,root,root) %{_sysconfdir}/%{NAME}.d/system/*
 %attr(0644,root,root) %{_exec_prefix}/etc/polkit-1/rules.d/%{NAME}.rules