For his playing company, Farrant combined his Windsor children with the Children of the Chapel Royal, then directed by William Hunnis. Relatively little is known of their repertoire, except that it presumably included works by Farrant and perhaps Hunnis. The landlord More appears to have remained patient with this use of his property until shortly before Farrant's death in 1580, when More attempted to prove that his tenant had broken the lease. This attempt came to nothing; supported by a letter from Robert Dudley, the widow Ann Farrant was allowed to lease the theater to Hunnis. Hunnis continued to produce plays at the site until 1583, when he sold his lease to Henry Evans. There followed a confused period of legal actions involving Hunnis, Ann Farrant, Evans, and More. The result, apparently orchestrated by Edward de Vere, the Earl of Oxford, placed the theater under the control of Hunnis and de Vere's secretary, playwright John Lyly. Lyly's plays and others were, for a year or two, performed at the theatre before production at court. In 1585, however, More obtained a legal judgement voiding the original lease. The theatre was shut down after this judgement for more than a decade.
Three years later, Richard Burbage was able to lease the property to Henry Evans, the lawyer who had been among those ejected more than fifteen years earlier. Evans entered a partnership with Nathaniel Giles, Hunnis's successor at the Chapel Royal. They used the theatre for a commercial enterprise with a group called the Children of the Chapel, which combined the choristers of the chapel with other boys, many taken up from local grammar schools under colour of Giles's warrant to provide entertainment for the Queen. The dubious legality of these dramatic impressments led to a challenge from a father in 1600; however, this method brought the company some of its most famous actors, including Nathaniel Field and Salmon Pavy. The residents did not protest this use, probably because of perceived social differences between the adult and child companies.
While it housed this company, Blackfriars was the site of an explosion of innovative drama and staging. Together with its competitor, Paul's Children, the Blackfriars company produced plays by a number of the most talented young dramatists of Jacobean literature, among them Thomas Middleton, Ben Jonson, George Chapman, and John Marston. Chapman and Jonson wrote almost exclusively for Blackfriars in this period, while Marston began with Paul's but switched to Blackfriars, in which he appears to have been a sharer, by around 1605. In the latter half of the decade, the company at Blackfriars premiered plays by Francis Beaumont (The Knight of the Burning Pestle) and John Fletcher (The Faithful Shepherdess) that, although failures in their first production, marked the first significant appearance of these two dramatists, whose work would profoundly affect early Stuart drama. The new plays of all these playwrights deliberately pushed the accepted boundaries of personal and social satire, of violence on stage, and of sexual frankness. These plays appear to have attracted members of a higher social class than was the norm at the Bankside and Shoreditch theatres, and the admission price (sixpence for a cheap seat) probably excluded the poorer patrons of the amphitheatres. Prefaces and internal references speak of gallants and Inns of Court men, who came not only to see a play but also, of course, to be seen; the private theatres sold seats on the stage itself.
The Blackfriars playhouse was also the source of other innovations which would profoundly change the nature of English commercial staging: it was among the first commercial theatrical enterprises to rely on artificial lighting, and it featured music between acts, a practice which the induction to Marston's The Malcontent (1604) indicates was not common in the public theatres at that time.
In the years around the turn of the century, the children's companies were something of a phenomenon; a reference in Hamlet to "little eyasses" suggests that even the adult companies felt threatened by them. By the later half of that decade, the fashion had changed somewhat. In 1608, Burbage's company (by this time, the King's Men) took possession of the theatre, which they still owned, this time without objections from the neighbourhood. There were originally seven sharers in the reorganised theatre: Richard Burbage, William Shakespeare, Henry Condell, John Heminges, and William Sly, all members of the King's Men, plus Cuthbert Burbage and Thomas Evans, agent for the theatre manager Henry Evans. Sly, however, died soon after the arrangement was made, and his share was divided among the other six.
After renovations, the King's Men began using the theatre for performances in 1609. Thereafter the King's Men played in Blackfriars for the seven months in winter, and at the Globe during the summer. Blackfriars appears to have brought in a little over twice the revenue of the Globe; the shareholders could earn as much as £13 from a single performance, apart from what went to the actors.
In the reign of Charles I, even Queen Henrietta Maria was in the Blackfriars audience. On May 13, 1634 she and her attendants saw a play by Philip Massinger; in late 1635 or early 1636 they saw Lodowick Carlell's Arviragus and Philicia, part 2; and they attended a third performance in May of 1636.
The theatre closed at the onset of the English Civil War, and was demolished on August 6, 1655.