Long-simmering tensions between Mascis and Barlow, who rarely spoke to each another, hastened the latter's exit from the group after 1988's superb Bug. After his dismissal, Barlow turned his focus to Sebadoh, a side project that he had begun with multi-instrumentalist Eric Gaffney several years prior. While Dinosaur Jr. had won acclaim for its monolithic guitar sound, Sebadoh was initially conceived as a bare-bones, deliberately low-fidelity home recording project spotlighting Barlow's pensive, emotional songs and Gaffney's noise collages. Over the course of a barrage of singles and sprawling albums like 1989's The Freed Man, 1990's Weed Forestin, and 1991's Sebadoh III, Sebadoh -- which later added drummer/songwriter Jason Loewenstein -- matured and expanded its scope; while still defiantly anti-commercial, the group's music grew more complex and fully developed, and moved progressively away from its primitive origins.

No doubt as a reaction to Sebadoh's growth, Barlow started the first of many concurrent side projects, dubbed Sentridoh, and released the Losers cassette in 1991. For all intents and purposes a solo project, Sentridoh allowed the staggeringly prolific performer room to explore not only his shambling acoustic folk-pop but also whatever other ideas he felt like entertaining. A series of other releases followed, most of them on cassette, although the highlights were compiled on CD collections like 1994's Winning Losers: A Collection of Home Recordings, The Original Losing Losers, and Lou Barlow and His Sentridoh, which featured the sublime love song "Forever Instant." Another Collection of Home Recordings, released under the name Lou Barlow & Friends and featuring Bob Fay (Gaffney's replacement in Sebadoh), appeared in 1995.

In 1994, Barlow also teamed with fellow singer/songwriter John Davis in the Folk Implosion, another home-recording outlet (albeit one marked by odd stylistic detours into blue-eyed funk, Lennon-esque pop, and noise abrasion). Following a series of EPs and singles, in 1995 the Folk Implosion recorded a number of songs for filmmaker Larry Clark's acclaimed feature Kids; the soundtrack's infectious "Natural One" became a surprise Top 40 hit later that year, further raising Barlow's increasingly high profile. After Sebadoh's acclaimed 1996 LP Harmacy, Barlow recorded the Folk Implosion's Dare to Be Surprised for release in the spring of 1997. A steady flow of Sebadoh, Folk Implosion, and collaborative records continued in the years to come, as did the solo efforts Emoh and Goodnight Unknown.