this post was submitted on 31 Aug 2025
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Linux
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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.