diff --git a/modules/flatpaks/files/bin/system-flatpak-setup b/modules/flatpaks/files/bin/system-flatpak-setup
new file mode 100755
index 0000000..1bdddd3
--- /dev/null
+++ b/modules/flatpaks/files/bin/system-flatpak-setup
@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+# Script Version
+VER=1
+VER_FILE="/etc/ublue-os/system-flatpak-configured"
+VER_RAN=$(cat $VER_FILE)
+
+# Run script if updated
+if [[ -f $VER_FILE && $VER = $VER_RAN ]]; then
+  echo "Flatpak setup v$VER has already ran. Exiting..."
+  exit 0
+fi
+
+# Opt out of and remove Fedora's flatpak repo
+if grep -qz 'fedora' <<< $(flatpak remotes); then
+  /usr/lib/fedora-third-party/fedora-third-party-opt-out
+  /usr/bin/fedora-third-party disable
+  flatpak remote-delete fedora --force
+fi
+
+# Set up system Flathub if not already installed
+flatpak remote-add --if-not-exists --system flathub https://flathub.org/repo/flathub.flatpakrepo
+
+# In case fedora flatpak repo is already removed, but Flathub was left disabled by mistake
+flatpak remote-modify flathub --enable --system --title="Flathub (System)"
+
+# Lists of flatpaks
+FLATPAK_LIST=$(flatpak list --columns=application)
+INSTALL_LIST=$(cat /etc/flatpak/system-install)
+REMOVE_LIST=$(cat /etc/flatpak/system-remove)
+
+# Install flatpaks in list
+if [[ -n $INSTALL_LIST ]]; then
+  for flatpak in $INSTALL_LIST; do
+    if grep -qvz $flatpak <<< $FLATPAK_LIST; then
+      flatpak install --system --noninteractive flathub $flatpak
+    fi
+  done
+fi
+
+# Remove flatpaks in list
+if [[ -n $REMOVE_LIST ]]; then
+  for flatpak in $REMOVE_LIST; do
+    if grep -qz $flatpak <<< $FLATPAK_LIST; then
+      flatpak remove --system --noninteractive $flatpak
+    fi
+  done
+fi
+
+# Prevent future executions
+echo "Writing state file"
+mkdir -p /etc/ublue-os
+echo $VER > $VER_FILE
\ No newline at end of file
diff --git a/modules/flatpaks/files/bin/user-flatpak-setup b/modules/flatpaks/files/bin/user-flatpak-setup
new file mode 100755
index 0000000..e068f67
--- /dev/null
+++ b/modules/flatpaks/files/bin/user-flatpak-setup
@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+# Script Version
+VER=1
+VER_FILE="$HOME/.config/ublue-os/user-flatpak-configured"
+VER_RAN=$(cat $VER_FILE)
+
+# Run script if updated
+if [[ -f $VER_FILE && $VER = $VER_RAN ]]; then
+  echo "Flatpak setup v$VER has already ran. Exiting..."
+  exit 0
+fi
+
+# Setup Flathub
+if grep -qz 'fedora' <<< $(flatpak remotes); then
+  flatpak remote-delete --user fedora --force
+fi
+flatpak remote-add --if-not-exists --user flathub https://flathub.org/repo/flathub.flatpakrepo
+
+# Lists of flatpaks
+FLATPAK_LIST=$(flatpak list --columns=application)
+INSTALL_LIST=$(cat /etc/flatpak/user-install)
+REMOVE_LIST=$(cat /etc/flatpak/user-remove)
+
+# Install flatpaks in list
+if [[ -n $INSTALL_LIST ]]; then
+  for flatpak in $INSTALL_LIST; do
+    if grep -qvz $flatpak <<< $FLATPAK_LIST; then
+      flatpak install --user --noninteractive flathub $flatpak
+    fi
+  done
+fi
+
+# Remove flatpaks in list
+if [[ -n $REMOVE_LIST ]]; then
+  for flatpak in $REMOVE_LIST; do
+    if grep -qz $flatpak <<< $FLATPAK_LIST; then
+      flatpak remove --user --noninteractive $flatpak
+    fi
+  done
+fi
+
+# Prevent future executions
+echo "Writing state file"
+mkdir -p $HOME/.config/ublue-os/
+echo $VER > $VER_FILE
\ No newline at end of file
diff --git a/modules/flatpaks/files/systemd/system/system-flatpak-setup.service b/modules/flatpaks/files/systemd/system/system-flatpak-setup.service
new file mode 100644
index 0000000..ae71aaa
--- /dev/null
+++ b/modules/flatpaks/files/systemd/system/system-flatpak-setup.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=Manage system flatpaks
+Documentation=https://github.com/ublue-os/endlish-oesque/issues/10
+Wants=network-online.target
+After=network-online.target
+
+[Service]
+Type=oneshot
+ExecStart=/usr/bin/system-flatpak-setup
+Restart=on-failure
+
+[Install]
+WantedBy=multi-user.target
\ No newline at end of file
diff --git a/modules/flatpaks/files/systemd/user/user-flatpak-setup.service b/modules/flatpaks/files/systemd/user/user-flatpak-setup.service
new file mode 100644
index 0000000..89a3fdc
--- /dev/null
+++ b/modules/flatpaks/files/systemd/user/user-flatpak-setup.service
@@ -0,0 +1,10 @@
+[Unit]
+Description=Configure Flatpaks for current user
+Requires=xdg-desktop-autostart.target
+
+[Service]
+Type=simple
+ExecStart=/usr/bin/user-flatpak-setup
+
+[Install]
+WantedBy=default.target
\ No newline at end of file
diff --git a/modules/flatpaks/flatpaks.sh b/modules/flatpaks/flatpaks.sh
index 8b8d147..6dd33b1 100644
--- a/modules/flatpaks/flatpaks.sh
+++ b/modules/flatpaks/flatpaks.sh
@@ -3,6 +3,11 @@
 # Tell build process to exit if there are any errors.
 set -oue pipefail
 
+export FLATPAKS_MODULE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+
+cp -r "$FLATPAKS_MODULE_DIR"/files/bin/* /usr/bin/
+cp -r "$FLATPAKS_MODULE_DIR"/files/systemd/* /usr/lib/systemd/
+
 SYS_INSTALL_LIST=/usr/etc/flatpak/system-install
 SYS_REMOVE_LIST=/usr/etc/flatpak/system-remove
 USER_INSTALL_LIST=/usr/etc/flatpak/user-install