The Athletic Bilbao midfielder has long been linked with a move away from San Mames, and will become the most expensive signing in the history of the Bundesliga.
The Spain international has long been linked with a move to the Allianz Arena, with the Bavarians looking to bolster their midfield options ahead of the start of the new season.
The transfer was triggered after Bayern activated a €40m buy-out clause in Martinez's contract, despite Die Roten apparently being reluctant to meet the fee - a German transfer record.
It appears that Martinez was keen on the move being finalised however, as under the terms of the deal he will allegedly give up €2m of his annual salary.
The versatile 23 year-old, who can play either as a central midfielder or defender, will sign a five-year contract, meaning he stands to lose €10m overall.
Bayern have already added Claudio Pizarro, Mario Mandzukic and Xherdan Shaqiri to their ranks this summer, as they look to wrestle the Bundesliga title from Borussia Dortmund.
Bayern were also hoping to sign Bayer Leverkusen midfieler Lars Bender during the summer transfer window, only for both player and club to rebuff their advances.