On January 15, 2000, Shaffer married Stephanie Roush. Together, they had a daughter, Carmella Star Shaffer (born on June 23, 2001). In 2004, Shaffer and Roush got divorced. Shaffer then started to date the Albanian American actress and model, Evis Xheneti in 2005. They were married on January 2, 2012, in Paris, France. They have three children together: D’Angelo DraXon Shaffer (born on November 7, 2012), Rocky Rebel Shaffer (born on August 20, 2015), and Heart Hera Shaffer (Born on August 7, 2019).

On February 22, 2005, Brian “Head” Welch left the band. Shaffer accepted his friend’s choice and the two remained on good terms. When drummer David Silveria left the band, Munky said in an interview that he had a strong friendship with him and was very sad to hear that he had to leave.

Shaffer predominantly uses Ibanez guitars, most often his signature model the Ibanez Apex 7-string model and Mesa Boogie Triple Rectifier & Diezel guitar amplifier. Like Brian did before leaving the band in 2005, he uses many pedals and effects to shape the distinct Korn sound. Munky describes his live pedal board as a “spaceship” because of the large, diverse quantity of effects he uses.

In 2006, Shaffer founded Emotional Syphon Records to give daring and diverse bands a chance to be heard. The first bands to be signed were Droid and Monster In The Machine, however Shaffer says he does not want to limit himself to only releasing metal acts but to create a multi-genre label.

On March 4, 2008, it was announced that Shaffer would be releasing a solo record on August 8, 2008 with his solo band Fear and The Nervous System which would feature Munky doing vocals and guitars, Brooks Wackerman of Bad Religion (who also performed on Korn’s 8th album) on drums, Leopold Ross on guitars and programming, Bill Gould of Faith No More fame, and Zac Baird (Korn’s keyboardist) on keyboards and programming. The record would be produced by Munky and Ross Robinson. Guitarist and friend Wes Borland originally recorded guitars for two songs on the album but they would not make the final cut. Borland also created cover art which would still be used on the album. The band’s debut album was originally due out August 8, 2008 but was pushed back multiple times until its release in 2011.

On Modlife in October, 2009 (Korn.com), Shaffer explained that he would not be doing vocals on the Fear and the Nervous System album because he is not “very good at singing.” It was later announced that Steve Krolikowski of Repeater would be handling vocal duties.

On an interview about Welch’s departure, Shaffer said he felt pressure, because they were always working together, writing songs, and creating albums. But when Welch left, he had to write all the guitar parts into one part, so Korn could play live, and he continued to play like that until Korn got a backing guitarist. Welch officially returned to the band on May 2, 2013 to work on the album The Paradigm Shift that was released in October 2013.