In 1993, following the fall of the USSR, Mr. Fomenko founded his own theatre, the Pyotr Fomenko Workshop Theater, creating a company from students at Moscow's theatre academy, where he also taught. There, he staged innovative approaches to works by Shakespeare, Chekhov and other classics. The company moved into its own quarters in 2000. Before creating his own home, Mr. Fomenko frequently butted heads with the Communist officials who monitored artistic efforts for signs of political dissent, and found his productions too modernist and free-thinking for their tastes. When staging plays in Moscow became too troublesome, he moved to then-Soviet Georgia, and later to Leningrad in the 1970s, eventually taking the helm of the Leningrad Comedy Theater. He lost the job in 1981 after another confrontation with authorities.

Having begun his career as an actor, studying at the Moscow Arts Theatre, he went on to stage more than 60 plays over his career, a few of which were presented at Lincoln Center. His 1958 debut as a director was Konstantin Finn's A Troubled Legacy at the Malaya Bronnaya Theater in Moscow. His final production was Triptych in 2009. His rendition of Alexander Ostrovsky's The Forest was seen at the Comedie Francaise in Paris in 2003. He also directed three feature films and made ten films for television.

At his own theatre, his hit productions included One Absolutely Happy Village (2000), Family Happiness (2000), The Mad Woman from Chaillot (2001), War and Peace (2001) and Egyptian Nights (2002). He said his job sometimes gave him "moments of pure happiness when tears would well up in my eyes."