Following his departure from Grisman's group, Marshall continued to work with fiddler Anger as a duo and, along with pianist Barbara Higbie and bassist Michael Manring, in a folk/chamber music group, Montreux. Marshall and Anger also collaborated, along with bassist Todd Phillips, banjo player Tony Trischka, and guitarist David Grier, in a bluegrass/jazz/classical/folk group, Psychograss. Marshall co-founded the Modern Mandolin Quartet and plays Brazilian music with Choro Famoso. Marshall has also periodically collaborated with Edgar Meyer, Jerry Douglas, Mark O'Connor, and Sam Bush in a bluegrass superband, Strength in Numbers. Marshall has produced numerous albums including recordings by Laurie Lewis, Alison Brown, Jennifer Berezan, and Tony Furtado.

Marshall's first solo album, 1989's Gator Strut, spotlighted his jazz-meets-bluegrass approach, and the follow-up, 1997's Brasil: Duets (reissued as Brazil: Duets in 2005), focused on the Brazilian influences on his music, featuring duets with Edgar Meyer, Michael Manring, and Béla Fleck. In 2003, Marshall teamed up with mandolinist Chris Thile to release Into the Cauldron, a fine record of duets between the two exploring everything from classical and traditional music to contemporary numbers written in collaboration. The year 2003 also saw the release of Serenata (by the duo of Marshall and pianist Jovino Santos Neto) on the newly formed Adventure Music label, dedicated to the exploration of Brazilian and diverse other musics. Subsequent releases on Adventure Music have included 2004's Mike Marshall & Choro Famoso, 2006's New Words (Novas Palavras) by Marshall and Hamilton De Holanda, 2007's Mike Marshall and Darol Anger with Vasen, 2009's Mike Marshall's Big Trio, and 2010's Caterina Lichtenberg and Mike Marshall, the latter pairing Marshall with current wife Lichtenberg, also a mandolinist.