In 2000, the company's first season consisted of productions of King Lear and A Midsummer Night's Dream. These were well received by critics such as Toby O'Connor Morse of The Independent, who commented on Lear: "One of the finest productions of Shakespeare – or any other playwright for that matter – seen in Bristol in years". On A Midsummer Night's Dream, Lyn Gardner of The Guardian commented: For the 2001 season, the company paired Measure for Measure with Coriolanus. Both productions were well received; Susannah Clapp of The Observer, reviewing Measure for Measure, stated: and on Coriolanus, Jeremy Kingston of The Times described the company as "one of the most exciting theatre companies in the land." For their third season, The Winter's Tale accompanied Twelfth Night. John Peter of The Sunday Times said of The Winter's Tale, "The costumes are striking and the props are few. Hilton's production, with the audience on four sides, is clean, clear and swift." and Lyn Gardner on Twelfth Night described the production style: The 2003 season productions of Troilus and Cressida and As You Like It were praised by critics, who noted that they "differ both from the RSC showcase efforts and the worthy but often laboured school curriculum ad-hoc companies." and
It is tiresome to have to use a small, unsubsidised company in the suburbs of Bristol to beat the great RSC about the head, but one lesson Boyd and his team might learn from the Tobacco Factory's As You Like It is that it is time to return to basics. Stop spending money on big, ugly sets. Concentrate your mind on the space, the actors, the words. If you have spare money, spend it on costumes. Those were the priorities of the Elizabethan managers.
2004 brought an end to the initial five-year plan, with productions of Macbeth and Middleton's The Changeling, which, after a spring run in Bristol, transferred to the Barbican Centre in London for a five-week run in the autumn. In May 2004 the company was reborn as a charity as it now continues, named Shakespeare at the Tobacco Factory 2004 Limited. This new status allowed charitable donations and an element of subsidy to be sought. In subsequent years the company has produced many more Shakespeare plays, as well as Anton Chekhov's The Cherry Orchard and Uncle Vanya, and Molière's The Misanthrope. Jonathan Miller was guest director for a 2008 production of Hamlet. Polinina Kalinina joined the company as the second guest director in 2015 for the production of .