On January 18, 2007, Lopez and Marx again collaborated to write four of the songs for the hit TV show Scrubs on the show's 123rd episode titled "My Musical." TV Guide named the episode one of the best 100 TV show episodes of all time in 2009. Lopez, along with Jeff Marx, was recognized with an Emmy nomination for the song "Everything Comes Down to Poo" from the above mentioned episode.Stephanie D'Abruzzo, who originated the roles of Kate Monster and Lucy the Slut in Avenue Q, guest-starred in the episode.
In 2005, Lopez began working on a new musical project with Matt Stone and Trey Parker, the creators of South Park, a series which, in 2003, Lopez had mentioned as a partial inspiration for Avenue Q.The Book of Mormon premiered on Broadway at the Eugene O'Neill Theatre on March 24, 2011, following previews from February 24. The show received numerous theater accolades, including the 2011 Tony for Best Musical, as well as two more Tony Awards for Lopez: Best Original Score and Best Book of a Musical. The production's original cast recording also earned Lopez the Grammy Award for Best Musical Theater Album.
In 2011, Lopez again worked with Matt Stone and Trey Parker on the South Park episode "Broadway Bro Down".
Lopez also co-wrote two songs for the Disney Channel animated series Phineas and Ferb. They are "Aerial Area Rug" for the episode "Magic Carpet Ride" and "Fly On the Wall" for the episode of the same name.
Lopez and his wife are currently creating a new musical titled Up Here. Lopez describes Up Here as "It's kind of like Annie Hall meets Cirque du Soleil. It's a romantic comedy with a huge theatrical twist." The couple are also working on another musical, Disney's Bob the Musical, with Allan Loeb writing the story.
During his participation in the 1998 Lehman Engel's Workshop, Robert Lopez met and began dating lyricist Kristen Anderson. As described in a 2003 The New York Times profile, the pair, struggling in a cash-strapped post-college period that recalls the storyline of Avenue Q's Princeton and Kate Monster, "live[d] in Astoria, Queens, [drove] a 1989 Buick and survive[d] on fast food".
The couple married in 2003 and they have two daughters; Katie and Annie, who both had voice parts in Frozen.