As documented on the "Criminal Minds" Fandom site, Agent Hotchner mentions in the Season 10 premiere that Mateo Cruz is overseas on assignment, which we see later in the season for the back-door pilot for "Criminal Minds: Beyond Borders," and one episode of the spin-off itself. However, after these appearances, Cruz is never seen or mentioned again.
Redditor u/CJaneNorman also asked about Cruz's disappearance on the "Criminal Minds" Subreddit, and some fellow users had some explanations, largely suggesting that scheduling issues with actor Esai Morales are what led to the character's sudden departure. Morales, a highly accomplished actor, appeared in many other projects around the same time of his role on "Criminal Minds," including "The Brink," "From Dusk Til Dawn: The Series," and "How To Get Away With Murder," so it's quite plausible he simply wasn't available to continue on the show.
However, his character's disappearance was less of an issue when Assistant Director of National Security Linda Barnes (Kim Rhodes) shows up in Season 13 as the new boss and tries to restructure the BAU. The writing team at "Criminal Minds" has never shared definitively what happened to Cruz, so it's up to dedicated fans to theorize where the character ended up. However, we think it's likely the agent continued his work overseas, chasing unsubs wherever the job led him.
