Of all such monopolies the university, by the power given to it in the charter of 1534 to print omnimodos libros, had been made nominally independent, and it was therefore inevitable that disputes should arise; furthermore, there being as yet no regularised law of copyright, such disputes were likely to be most violent when there was competition in the sale, as well as in the printing, of a text-book.

Thus when John Legate, himself a freeman of the Stationers' Company, printed an edition of Terence for the use of scholars in 1589 and sent copies to be sold in London, the Stationers quickly confiscated them; on their part, the Stationers were at the same time contemplating another pirated edition of Thomas's Dictionary. The university made its usual, dignified complaint to Lord Burghley.

Again, in 1591, Legate, who had in that year produced the first English bible printed at Cambridge, was accused of infringing the monopoly of Barker and Day, the privileged printers. In their reply to the charge, the Vice-Chancellor and Heads of Houses whilst hinting that the doctrine "that the prince by virtue of prerogative may, by a later grant, either take away or abridge a former" is not only "against the rule of natural equity" but also "dangerous to all degrees, opening a way to the overthrow of all patents and privileges," base their appeal upon an ad misericordiam, with a final reminder of the charter and its ratification; in particular, they emphasise the plight of the printer himself:

The suit which they [the Stationers] have made unto your lordship for the stay of our printer until the next term, is so prejudicial to the poor man, as if they should prevail therein, it could not but tend to his utter undoing; especially Sturbridge-fair now drawing near; being the chiefest time wherein he hopeth to reap greatest fruit of this his travail[23].

Similarly, in 1596, Legate was charged—this time by the Ecclesiastical Commissioners—with infringing the right of the Queen's patentees by printing the Grammar and Accidence. The Vice-Chancellor was required to collect all copies printed at Cambridge and to take bond with surety in £100 of each of the university printers not to print either book without leave. Some months later the Vice-Chancellor reported to the Archbishop that search had been made "by honest men sworn who said upon their oath that there were no such books printed here." This is the last we hear of such disputes for some time, but it is clear that the university jealously guarded its right of selling, as well as of printing, books, since in 1592 J. Tidder, of London, was sued in the Vice-Chancellor's Court for selling books in the Cambridge market[24].

In the later part of his career Legate became intimately associated with the London stationers. An entry in the Stationers' Registers under the date 1 August, 1597, shows that his official position was then recognised:

Whereas John legat hathe printed at Cambridge by Aucthoritie of the vniuersitie there a booke called the Reformed Catholike: This seid booke is here Registred for his copie so that none of this Company shall prynt yt from hym. Provided that this entrance shalbe voyd yf the seid booke be not Aucthorised by the seid vniuersitie as he saieth it is, vjd.[25]

Legate married the daughter of Christopher Barker and became Master of the Stationers' Company in 1604. He left Cambridge in 1609 and after that date all books printed by him have London on the title-page; the title, however, of "printer to the university" he retained until his death in 1620.

In Cambridge he rented a shop for 5s per annum in St Mary's parish from 1591 to 1609, probably the same house in the Regent Walk as that in which Thomas had lived, and was the first printer to use the device Alma Mater Cantabrigia with the motto Hinc Lucem et Pocula Sacra surrounding it.

In partnership with Legate was John Porter. There is no record of his appointment, but it is evident that he was one of the university stationers appointed under the charter. In 1593 we find him associated with Legate in the prosecution of John Tidder and several books of 1595 and other dates are described as printed for him and John Legate[26].