diff --git a/.github/workflows/reusable-build-iso-anaconda-webui.yml b/.github/workflows/reusable-build-iso-anaconda-webui.yml
index d1b64c0b7..7f4e66eb4 100644
--- a/.github/workflows/reusable-build-iso-anaconda-webui.yml
+++ b/.github/workflows/reusable-build-iso-anaconda-webui.yml
@@ -45,6 +45,12 @@ jobs:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
+      - name: Checkout common repo
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        with:
+          repository: get-aurora-dev/common
+          path: common
+
       - name: Setup Just
         uses: extractions/setup-just@e33e0265a09d6d736e2ee1e0eb685ef1de4669ff # v3
 
@@ -53,13 +59,6 @@ jobs:
         run: |
           just check
 
-      - name: Checkout Common Repo
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
-        with:
-          repository: get-aurora-dev/common
-          ref: main
-          path: common
-
       - name: Format image ref
         id: image_ref
         env:
@@ -73,12 +72,20 @@ jobs:
           echo "artifact_format="$image_name-${{ matrix.image_version }}-webui-$(uname -m)"" >> "${GITHUB_OUTPUT}"
           echo "kargs=$KARGS" >> "${GITHUB_OUTPUT}"
 
+      - name: Generate titanoboa-compatible file list
+        id: flatpak_list
+        run: |
+          set -eoux pipefail
+          FILE_LIST="$(mktemp)"
+          cat common/system_files/shared/usr/share/ublue-os/homebrew/system-flatpaks.Brewfile | grep -v '#' | grep -F -e "flatpak" | sed 's/flatpak //' | tr -d '"' | tee "${FILE_LIST}"
+          echo "file_list_path=${FILE_LIST}" | tee "${GITHUB_OUTPUT}"
+
       - name: Build ISO
         id: build
         uses: ublue-os/titanoboa@main
         with:
           image-ref: ${{ steps.image_ref.outputs.image_ref }}:${{ matrix.image_version }}
-          flatpaks-list: ${{ github.workspace }}/common/flatpaks/system-flatpaks.list
+          flatpaks-list: ${{ steps.flatpak_list.outputs.file_list_path }}
           hook-post-rootfs: ${{ github.workspace }}/iso_files/configure_iso_anaconda-webui.sh
           kargs: ${{ steps.image_ref.outputs.kargs }}
 
diff --git a/AGENTS.md b/AGENTS.md
index d92d68907..30d81ff3f 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -32,7 +32,6 @@ This document provides essential information for coding agents working with the
 - `.github/workflows/` - Comprehensive CI/CD pipelines
 - `just/` - Additional Just recipes for apps and system management
 - `brew/` - Homebrew Brewfile definitions for various tool collections
-- `flatpaks/` - Flatpak application lists
 - `iso_files/` - ISO installation configurations
 
 ### Architecture
@@ -173,7 +172,6 @@ The repository uses mandatory pre-commit validation:
 - `reusable-build.yml` - Core build logic for all image variants
 - `generate-release.yml` - Generates release artifacts and changelogs
 - `validate-brewfiles.yml` - Validates Homebrew Brewfile syntax
-- `validate-flatpaks.yml` - Validates Flatpak list files
 - `clean.yml` - Cleanup old images and artifacts
 - `moderator.yml` - Repository moderation tasks
 
diff --git a/Containerfile b/Containerfile
index 8fcd64f08..0a96a692f 100644
--- a/Containerfile
+++ b/Containerfile
@@ -15,7 +15,6 @@ COPY /build_files /build_files
 COPY /iso_files /iso_files
 
 # https://github.com/get-aurora-dev/common
-COPY --from=common /flatpaks /flatpaks
 COPY --from=common /logos /system_files/shared
 COPY --from=common /system_files /system_files
 COPY --from=common /wallpapers /system_files/shared
diff --git a/build_files/shared/build.sh b/build_files/shared/build.sh
index 99088a204..c39d449f4 100755
--- a/build_files/shared/build.sh
+++ b/build_files/shared/build.sh
@@ -4,9 +4,6 @@ set -eoux pipefail
 
 echo "::group:: Copy Files"
 
-# Copy ISO list for `install-system-flatpaks`
-install -Dm0644 -t /etc/ublue-os/ /ctx/flatpaks/*.list
-
 # We need to remove this package here because lots of files we add from `{projectbluefin,get-aurora-dev}/common` override the rpm files and they also go away when you do `dnf remove`
 # TODO: this can be removed whenever we stop doing FROM ublue-os/kinoite-main
 dnf remove -y ublue-os-just ublue-os-signing ublue-os-udev-rules ublue-os-luks ublue-os-update-services