Stubblefield currently lives in Madison, Wisconsin. Recently Clyde Retired from the Monday shows, leaving the band in the hands of his nephew Brett Stubblefield. His health prevented the funky drummer from continuing his over 20 years of playing music in downtown Madison near the capitol. He played every Monday night with his Madison band, The Clyde Stubblefield Band, featuring his long time friend and keyboard/organ player Steve "Doc" Scaggs, along with soulful vocalists Charlie Brooks, and Kari Daley, as well as a powerful five-piece horn section and supporting band. He also plays funk festivals with Bootsy Collins, Maceo Parker, or Jabo.
In 1995 he played on two tracks ("Queer" and "Not my idea") on the self-titled album by the rock band Garbage, led by fellow Madison resident Butch Vig.
In recent years Stubblefield has collaborated frequently with another former James Brown drummer, John "Jabo" Starks. As the Funkmasters, they released an album in 2001 called Find The Groove. and COME GET SUMMA THIS. Starks and Stubblefield also appear on a drumming instructional video.
Stubblefield and Starks played on "Funk For Your Ass," a CD by fellow James Brown Orchestra alum Fred Wesley which was recorded and mixed by Bob Both. This album was released in 2008 by Columbia Entertainment Music, Inc. in Tokyo.
Jab'o and Clyde joined Bootsy Collins in Covington, KY/Madison Theater on 22 December 2007 for the first Tribute to James Brown.
In November 2008 Toontrack Music announced the release of an expansion to their EZdrummer drum sampler software, titled "Funkmasters", with samples and MIDI recorded by Stubblefield and Starks.
As of June 2009, Stubblefield is in need of a kidney transplant and undergoes dialysis treatments. Bands throughout Madison are making a strong effort to organize and play fundraiser events, donating the event proceeds to go toward supplementing Stubblefield's dialysis treatment and subsequent medical bills.
On August 24, 2012, Stubblefield gave an autobiographical talk and played some of his favorite beats at the MadisonRuby software conference in Madison, WI. Earlier in the day, there was a talk by fellow historic drummer, Martin Atkins.