Sahanaja worked with Brian Wilson and Van Dyke Parks in sequencing and arranging the fragments of Wilson's legendary, ill-fated Smile album into a completed work. The album, started by Wilson in 1966 with the Beach Boys, was finally completed in 2004 as a solo artist. Wilson, Sahanaja and the rest of Wilson's band performed Brian Wilson Presents Smile both live, and in the studio.
Along with his duties leading Wilson's touring band, Sahanaja performed alongside The Zombies on the 40th anniversary tour of their 1968 album Odessey and Oracle. He later performed with Heart at the "Dreamboat Annie Live" concert, writing string arrangements, while also playing percussion, keyboards, and singing background vocals. In 2012, Sahanaja appeared on The Beach Boys' reunion album, That's Why God Made the Radio, and the subsequent anniversary tour, playing keyboards and providing backing vocals. He also sings lead on "Darlin'", originally sung by Carl Wilson, during the concerts.