From the unison bass-sax line in the opening measures of the first tune "Liar's Web," the compatibility of Formanek and Berne is apparent; they would continue a fruitful musical partnership for the remainder of the decade. Extended Animation also reveals Formanek's skill in writing compositions of greater length and complexity than the generally shorter vignettes on Wide Open Spaces. The same year that Extended Animation was released, Formanek, Berne, and Hirshfield entered the studio to record Loose Cannon for Italian producer Giovanni Bonandrini's Soul Note label. This trio session, with bass and sax squarely in the spotlight, further cemented the nascent Formanek-Berne relationship. Loose Cannon was released in 1993, as Formanek returned to the studio for another Enja session, this time with his largest group yet. The septet on Low Profile included Formanek and Berne along with trumpeter Dave Douglas, multi-reedist Marty Ehrlich, trombonist Ku-umba Frank Lacy, drummer Marvin "Smitty" Smith, and pianist Salvatore Bonafede. With its balance of high-energy improvisational passages and intricate ensemble arrangements, Low Profile was regarded by many critics as one of the strongest creative jazz CDs of 1994.

Meanwhile, Tim Berne decided to tap Formanek for Bloodcount, his quartet also featuring saxophonist/clarinetist Chris Speed and drummer Jim Black. In September 1994, the four musicians, plus guitarist Marc Ducret, recorded several nights of concerts for Stefan Winter's JMT label; the resulting music was released in 1995 on a trio of classic Bloodcount CDs: Lowlife, Poisoned Minds, and Memory Select. The demise of JMT came soon after, but Bloodcount continued to record (minus Ducret) for Berne's new Screwgun label. Formanek appears on three Bloodcount recordings issued by Screwgun: the Bloodcount Unwound three-CD box set (1996), as well as Discretion and Saturation Point (both 1997). Still under contract to Enja, Formanek recorded Nature of the Beast, his fourth album for the label, in 1996. The CD was released the following year and features a core quartet including trumpeter Douglas, trombonist Steve Swell, and a drummer with whom Formanek had been developing a particularly strong rapport: Bloodcount's Jim Black. Also making appearances on selected tracks were tenor saxophonist Tony Malaby, a relative newcomer to the New York creative improvising community, and both Berne and Speed. Everyone appears on the stunning, 12-minute "Thick Skin/Dangerous Crustaceans," sounding quite like an extended ensemble version of Bloodcount.

As the 1990s drew to a close, Berne put Bloodcount on hold, but Formanek continued his liaison with the saxophonist. They toured throughout the United States as a duo and in 1998 released the CD Ornery People on the Little Brother label. That same year, Screwgun issued Am I Bothering You?, a Formanek solo CD that fully reveals the bassist's improvisational skills and mastery of extended techniques. In addition, Formanek toured in 1998 as a member of drummer Gerry Hemingway's new American quartet, which also included trombonist Ray Anderson and tenor saxophonist Ellery Eskelin. On the 1999 Enja CD Relativity, Formanek appeared in a new collaborative trio with reedman Ehrlich and drummer Peter Erskine, drawing critical praise for his ability to maintain a propulsive groove while also providing the ensemble with plenty of room for abstract exploration. At the June 2000 Bell Atlantic Jazz Festival in New York City, Formanek premiered Northern Exposure, a new quartet with drummer Black, trumpeter Dave Ballou, and saxophonist Henrik Frisk. Despite all this activity, Formanek remained an in-demand session bassist throughout the 1990s, performing on CDs by leading creative jazz artists such as Jane Ira Bloom, Uri Caine, Marty Ehrlich, James Emery, Lee Konitz, Kevin Mahogany, the Mingus Big Band, the New York Jazz Collective, Daniel Schnyder, and Jack Walrath. By the year 2000, he had appeared on over 60 recordings as leader, collaborator, or sideman.

At the beginning of the new millennium, Formanek accepted a limited-time faculty appointment to the Jazz Studies Department at Baltimore's Peabody Institute, one of the oldest music conservatories in the U.S. and since 1977 a division of Johns Hopkins University. Two years later he was appointed as a full-time faculty member, and -- while continuing to participate in a number of recordings as a sideman -- he devoted much of his creative energy to the academic arena for the remainder of the decade, also receiving fellowships and commissions for the composition of new works. He re-emerged as a recording session leader in 2010 with the release of The Rub and Spare Change on the ECM label; in addition to Formanek on bass (and as composer), the quartet date featured saxophonist Berne, pianist Craig Taborn, and drummer Gerald Cleaver. Michael Formanek has proven that he can do it all: bassist, composer, educator, bandleader, and first-call sideman to many of the most highly regarded artists in creative jazz. Given his string of accomplishments, jazz fans can remain hopeful that Formanek has even more to offer in the years ahead.