diff --git a/contrib/ci/dependencies.xml b/contrib/ci/dependencies.xml
index 6cdc5d852..35001d7a3 100644
--- a/contrib/ci/dependencies.xml
+++ b/contrib/ci/dependencies.xml
@@ -1508,16 +1508,6 @@
       <package />
     </distro>
   </dependency>
-  <dependency type="build" id="flatpak-builder">
-    <distro id="flatpak">
-      <package />
-    </distro>
-  </dependency>
-  <dependency type="build" id="tree">
-    <distro id="flatpak">
-      <package />
-    </distro>
-  </dependency>
   <dependency type="build" id="libtss2-dev">
     <distro id="arch">
       <package>tpm2-tss</package>
diff --git a/contrib/ci/generate_dependencies.py b/contrib/ci/generate_dependencies.py
index 974a9ebc0..382ee8b32 100755
--- a/contrib/ci/generate_dependencies.py
+++ b/contrib/ci/generate_dependencies.py
@@ -55,7 +55,7 @@ if __name__ == "__main__":
         "-o",
         "--os",
         default=target,
-        choices=["fedora", "centos", "flatpak", "debian", "ubuntu", "arch"],
+        choices=["fedora", "centos", "debian", "ubuntu", "arch"],
         help="dependencies for OS",
     )
     args = parser.parse_args()
diff --git a/contrib/ci/generate_docker.py b/contrib/ci/generate_docker.py
index 80e83ed75..7390cb661 100755
--- a/contrib/ci/generate_docker.py
+++ b/contrib/ci/generate_docker.py
@@ -52,7 +52,7 @@ with open("Dockerfile", "w") as wfd:
                 replace = ""
             wfd.write(line.replace("%%%ARCH_PREFIX%%%", replace))
         elif line == "%%%INSTALL_DEPENDENCIES_COMMAND%%%\n":
-            if OS == "fedora" or OS == "flatpak":
+            if OS == "fedora":
                 wfd.write("RUN dnf --enablerepo=updates-testing -y install \\\n")
             elif OS == "centos":
                 wfd.write("RUN yum -y install \\\n")