diff --git a/docs/userguide.md b/docs/userguide.md
index 57af97e1..d1715568 100644
--- a/docs/userguide.md
+++ b/docs/userguide.md
@@ -21,6 +21,7 @@
 
 ## Applications Setup
 
+- **Flathub**: Installs / Uninstalls Flatpak and Flathub.
 - **Alacritty Setup**: Installs and configures Alacritty for you.
 - **DwmTitus Setup**: Sets up the Dwm window manager.
 - **Kitty Setup**: Installs and configures Kitty for you.
diff --git a/tabs/applications-setup/setup-flatpak.sh b/tabs/applications-setup/setup-flatpak.sh
new file mode 100644
index 00000000..749ddf1b
--- /dev/null
+++ b/tabs/applications-setup/setup-flatpak.sh
@@ -0,0 +1,91 @@
+#!/bin/sh -e
+
+. ../common-script.sh
+
+# Used to detect the desktop environment, Only used for the If statement in the setup_flatpak function.
+# Perhaps this should be moved to common-script.sh later on?
+detect_de() {
+    if [ -n "$XDG_CURRENT_DESKTOP" ]; then
+        case "$XDG_CURRENT_DESKTOP" in
+            *GNOME*)
+                DE="GNOME"
+                ;;
+            *KDE*)
+                DE="KDE"
+                ;;
+        esac
+    fi
+}
+
+# Install Flatpak if not already installed.
+setup_flatpak() {
+    if ! command_exists flatpak; then
+    printf "%b\n" "${YELLOW}Installing Flatpak...${RC}"
+        case "$PACKAGER" in
+            pacman)
+                $ESCALATION_TOOL "$PACKAGER" -S --needed --noconfirm flatpak
+                ;;
+            apt-get|nala)
+                $ESCALATION_TOOL "$PACKAGER" install -y flatpak
+                ;;
+            dnf)
+                $ESCALATION_TOOL "$PACKAGER" install -y flatpak # Fedora should have flatpak already installed, this is just a failsafe
+                ;;
+            zypper)
+                $ESCALATION_TOOL "$PACKAGER" install -y flatpak
+                ;;
+            yum)
+                $ESCALATION_TOOL "$PACKAGER" install -y flatpak
+                ;;
+            xbps-install)
+                $ESCALATION_TOOL "$PACKAGER" install -S flatpak
+                ;;
+            *)
+                printf "%b\n" "${RED}Unsupported package manager: $PACKAGER${RC}"
+                exit 1
+                ;;
+        esac
+        printf "%b\n" "Adding Flathub remote..."
+        $ESCALATION_TOOL flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+    else
+        if command -v flatpak >/dev/null 2>&1; then
+            if ! flatpak remotes | grep -q "flathub"; then
+                printf "%b\n" "${YELLOW}Detected Flatpak package manager but Flathub remote is not added. Would you like to add it? (y/n)${RC}"
+                read add_remote
+                case "$add_remote" in
+                    [Yy]*)
+                        printf "%b\n" "Adding Flathub remote..."
+                        $ESCALATION_TOOL flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+                        ;;
+                esac
+            else
+                # Needed mostly for systems without a polkit agent running (Error: updating: Unable to connect to system bus)
+                printf "%b\n" "${GREEN}Flathub already setup. You can quit.${RC}"
+            fi
+        fi
+    fi
+
+    if [ "$PACKAGER" = "apt-get" ] || [ "$PACKAGER" = "nala" ]; then
+        detect_de
+        # Only used for Ubuntu GNOME. Ubuntu GNOME doesnt allow flathub to be added as a remote to their store.
+        # So in case the user wants to use a GUI siftware manager they can setup it here
+        if [ "$DE" = "GNOME" ]; then
+            printf "%b\n" "${YELLOW}Detected GNOME desktop environment. Would you like to install GNOME Software plugin for Flatpak? (y/n)${RC}"
+            read install_gnome
+            if [ "$install_gnome" = "y" ] || [ "$install_gnome" = "Y" ]; then
+                $ESCALATION_TOOL "$PACKAGER" install -y gnome-software-plugin-flatpak
+            fi
+        # Useful for Debian KDE spin as well
+        elif [ "$DE" = "KDE" ]; then
+            printf "%b\n" "${YELLOW}Detected KDE desktop environment. Would you like to install KDE Plasma Discover backend for Flatpak? (y/n)${RC}"
+            read install_kde
+            if [ "$install_kde" = "y" ] || [ "$install_kde" = "Y" ]; then
+                $ESCALATION_TOOL "$PACKAGER" install -y plasma-discover-backend-flatpak
+            fi
+        fi
+    fi
+}
+
+checkEnv
+checkEscalationTool
+setup_flatpak
diff --git a/tabs/applications-setup/tab_data.toml b/tabs/applications-setup/tab_data.toml
index 0a9be9fb..fad13af5 100644
--- a/tabs/applications-setup/tab_data.toml
+++ b/tabs/applications-setup/tab_data.toml
@@ -1,5 +1,9 @@
 name = "Applications Setup"
 
+[[data]]
+name = "Setup Flatpak / Flathub"
+script = "setup-flatpak.sh"
+
 [[data]]
 name = "Alacritty"
 description = "Alacritty is a modern terminal emulator that comes with sensible defaults, but allows for extensive configuration. By integrating with other applications, rather than reimplementing their functionality, it manages to provide a flexible set of features with high performance. The supported platforms currently consist of BSD, Linux, macOS and Windows.\nThis command installs and condifures alacritty terminal emulator."
diff --git a/tabs/system-setup/system-update.sh b/tabs/system-setup/system-update.sh
index d5dcf08a..6bcaf99a 100755
--- a/tabs/system-setup/system-update.sh
+++ b/tabs/system-setup/system-update.sh
@@ -93,7 +93,18 @@ updateSystem() {
 
 updateFlatpaks() {
     if command_exists flatpak; then
-        flatpak update -y
+        printf "%b\n" "${YELLOW}Updating installed Flathub apps...${RC}"
+        installed_apps=$(flatpak list --app --columns=application)
+
+        if [ -z "$installed_apps" ]; then
+            printf "%b\n" "${RED}No Flathub apps are installed.${RC}"
+            return
+        fi
+
+        for app in $installed_apps; do
+            printf "%b\n" "${YELLOW}Updating $app...${RC}"
+            flatpak update -y "$app"
+        done
     fi
 }