The MFQ split up in 1966, and Yester began work as a solo artist and as a producer, with his wife Judy Henske, his brother Jim's band The Association, The Turtles, and Tim Buckley, for whom he produced Goodbye and Hello and Happy Sad. The following year he joined the Lovin’ Spoonful, replacing Zal Yanovsky, whom he also later worked with as producer, but in 1968 the Spoonful split up for 23 years. In 1969, Henske, Yester and Yanovsky put together the cult album Farewell Aldebaran, on which Yester played nearly a dozen different instruments. The following year Yester and Henske formed a new band, Rosebud, but the band dissolved in 1971; the couple then divorced.
Yester continued to work as a producer and/or arranger on albums by The Turtles, Pat Boone, Aztec Two Step, and Tom Waits, and in the 1970s also performed with The Association and the re-formed Modern Folk Quartet. In the mid 1980s he moved to Hawaii and formed a dance band called Rainbow Connection with his brother Jim, and Rainbow Rastasan (Rainbow Page).
In 1988 the MFQ began periodic touring of Japan, and have since recorded seven CDs for Japanese labels, including one (Wolfgang) using the music of Wolfgang Amadeus Mozart. In 1991 both Yester brothers joined a re-formed Lovin’ Spoonful with whom Jerry continues to tour. He now resides in the area of Harrison, Arkansas, where he's still producing, and arranging in his own studio, Willow Sound, and playing as a solo three nights a week in Eureka Springs, AR, at the Grand Central Hotel, and the Stone House.