Rolling Stone included Saunier alongside Brian Chippendale (of Lightning Bolt) and Zach Hill (of Hella, later Death Grips and the I.L.Y's) as together composing "a generation of trailblazing 21st-century avant-rock percussionists".

[12] Outside of Deerhoof, Saunier's bands include Mystical Weapons (a duo with Sean Lennon)[13][14] and a collaboration with Brian Chippendale, about which a documentary, Checking in at 20, was produced.

[15][16][17] He also formed Nervous Cop with drummer Zach Hill and harpist Joanna Newsom,[18] and bands with members of Erase Errata and Rainer Maria, soundtracked a film by Martha Colburn, and collaborated with Yonatan Gat on a reinterpretation of Antonín Dvořák's American Quartet.

[19][20][21] Saunier is a member of the indie rock supergroup Big Walnuts Yonder alongside bassist Mike Watt (Minutemen, fIREHOSE), guitarist Nels Cline (Wilco) and guitarist/vocalist Nick Reinhart (Tera Melos).

[31] In 2016, Saunier collaborated with American Brazilian composer Marcos Balter, in which they wrote songs for Deerhoof and Ensemble Dal Niente.