Handley was co-founder, with Alexis Snouffer, of the group which became "Captain Beefheart and his Magic Band". It was group-leader Snouffer who coaxed Handley from guitar to bass during the early rehearsals of the Magic Band.
Handley attended school with drummer P.G. Blakely, who was an early member of the group. He also spent time playing and recording with Zappa at Studio Z, where he had met Doug Moon and reunited with Snouffer who had returned to the scene.
Along with Snouffer, Handley had departed the group by the summer of 1968 and was briefly replaced by Gary "Magic" Marker for the early workings of "Trout Mask Replica".