(vanilla) mastodon does not have markdown, and content from other instances (marked up or not) get transmitted as HTML over the wire (and the mastodon API serves sanitized HTML to apps).
mastodon forks like glitch, and clones of the mastodon API like those on pleroma/akkoma and iceshrimp do serve the markdown source AFAIK, but unless OP’s looking to… idk, support MFM (which, on a non-web app would be difficult) I don’t really see the point in that.