Why MKV exists as an alternative to MP4
MKV (Matroska) was designed as an open, extremely flexible container that can hold essentially any video or audio codec, multiple audio tracks (different languages, commentary tracks), multiple subtitle tracks, and chapter markers — capabilities that MP4 either doesn't support at all or supports much less comprehensively. This is why MKV is the format of choice for high-quality video archiving, releases with multiple language options, and anything that needs more than a single video-and-audio stream.
The trade-off for that flexibility is compatibility: many phones, smart TVs, older media players, and platforms either don't support MKV at all or handle it inconsistently, especially compared to MP4's near-universal support.
What you give up by converting to MP4
Converting from MKV to MP4 typically means picking a single audio track and a single subtitle track (if any) to carry forward, since MP4 doesn't support MKV's multi-track flexibility the same way — this is a real loss if the original file had multiple language tracks or several subtitle options you wanted to preserve. It's worth deciding which specific track matters before converting, since the others won't automatically come along.
If preserving multiple tracks is essential, MP4 may not be the right destination format at all — some other container formats support multi-track audio and subtitles while still being more broadly compatible than MKV, depending on the specific use case.
When MP4 is genuinely the better choice despite the trade-off
If the destination is a device or platform that plays MP4 reliably but struggles with or rejects MKV entirely — many phones, some smart TVs, various upload platforms — converting is the practical fix regardless of what capability gets left behind. Simple playback needs (one video track, one audio track, no need for multiple subtitle options) lose nothing meaningful in the conversion, since MP4 handles that basic case just as well as MKV does.
Codec compatibility inside the conversion
MKV files can contain almost any video codec, including some that MP4 doesn't support as a container at all — if the source MKV uses a codec MP4 can't hold, a genuine re-encode to a compatible codec (typically H.264) is required rather than a simple container swap, which takes more processing time and carries the usual small quality trade-off of a real re-encode.