flatpak should be newer than apt, correct if wrong.
I first installed FFmpeg extension with extra codecs from flatpak, executed a ffmpeg command that returned: command not found.
I then thought the flatpak package, as the name states, is an extension that needs the apt version to be installed to work, so I executed sudo apt install ffmpeg and after downloading, the command worked.
Should I get rid of flatpak’s ffmpeg? Am I gaining functions with this package?
ffmpeg -version returns
ffmpeg version 7.1.1-1+b1 Copyright (c) 2000-2025 the FFmpeg developers built with gcc 14 (Debian 14.2.0-19)
You cannot run flatpak application by simply calling the binary.
Coming to your question, I suggest you to install ffmpeg directly from your Debian repo, this way you can get hardware acceleration or device specific benefits for encoding/decoding/transcoding.
You can keep the flatpak version if it is needed by some other flatpak applications. Normally one won’t interfere with the other.