Most of the scholars of the University were at first clerks or clergymen,in holy orders of some sort, and expecting careers in the Church or in the Civil Service (as diplomats, judges or officers of the royal household). To support them during their years of study, they looked for preferment in the Church (a benefice, a canonry, even a dignity in a cathedral), but as ordained clerks they were at first subject to the local ecclesiastical authorities, that is, the Archdeacon and the Bishop of Ely. Before the end of the fifteenth century, however, they had freed themselves from this, and were independent of all ecclesiastical authority except the Pope's. The Chancellor became an ecclesiastical judge in his own right, hearing all cases involving the morals or discipline of scholars, and proving the wills of all who died in residence. At about the same period, the Chancellor also provided scholars with a secular court to which they could resort for the trial of all civil and criminal cases except those concerning major crimes.

The Crown added to the University's independence. It introduced measures to protect scholars against exploitation by townsmen who had acquired market and toll rights which enabled them to raise the prices of food, fuel and candles. To counter this, the University was granted the right to proceed at law against market profiteers, and to enforce the conduct of assizes, or tests, of bread and ale by the town.

The acquisition of these powers continued to be a source of friction between town and gown (the University) until the nineteenth century. More immediately, it is thought that the attacks on University property in the town in 1381 were partly inspired by resentment of this interference.

If this is so, the attack was ill judged, since as a result of a Royal inquiry into the disturbances, the University was granted a jurisdiction which allowed the Chancellor not only to prosecute the profiteers, but also those falsifying weights and measures, endangering public health by the adulteration of food and drink, interrupting the supplies of fresh water, or wilfully introducing infection during epidemics of 'plague'. Further control of traders was allowed to the Chancellor with the grant of jurisdiction over law suits arising during markets and fairs. The last vestiges of these rights did not disappear until the nineteenth century, and the University retains even today certain responsibilities in connection with policing and licensing.