The left back has completed all the necessary details and becomes the first non-EU player at the club to receive a Spanish passport.
Villarreal have tried to obtain dual nationality for a number of players but each previous application has been turned down.
Arruabarrena has spent two years going through the process and now qualifies for Spanish citizenship.
He now ceases to occupy one of the non-EU berths at the club but Villarreal still have Brazilians Sonny Anderson and Marcos Senna.
However, at the beginning of the season, right back Juliano Belletti was able to get dual nationality when he qualified for an Italian passport.
