On November 24, 2006 at Cleveland's Quicken Loans Arena, Axl Rose called the Eagles of Death Metal (one of Guns N' Roses' opening acts) the "Pigeons of Shit Metal." Jesse Hughes, the Eagles of Death Metal's lead singer, told NME that Stinson took his bass off and threw it on the floor saying "Fuck you, that's it" and threatened to leave the band. Stinson did not leave Guns N' Roses; however, the Eagles of Death Metal were fired from the tour. On December 2, 2006, Stinson issued a statement reading, in part: "Eagles of Death Metal were a suggestion of mine a while ago. Turns out they were the wrong band for our crowd. They were booed and did not play for as long as they were scheduled to. ... In the past I have thrown my bass. I have never thrown it at Axl or anyone else in the band nor has anyone thrown my bass back at me... yet. Axl has been a dear friend to me for nine years. We have no problem communicating and wish that people would stay the fuck out of shit they don't know anything about."
In the fall of 2005, Tommy joined Soul Asylum for a few gigs in tribute to recently deceased bassist and founding member Karl Mueller. Stinson and Dave Pirner (founding member of Soul Asylum) were friends in high school in Minneapolis, MN. He also helped finish the rest of the recording for the album The Silver Lining released in 2006. He toured with them for a number of years when his schedule allowed for it, played on their 2012 Delayed Reaction album and was replaced permanently by Winston Roye in 2012 due to his lack of availability.