The Priory had always been famous for its piety, and in 1199, Hugh, who had been Prior there till 1186, was raised to be Abbot of Cluny itself.  This is interesting and important for we have thus an ex-Prior of Lewes as Abbot of Cluny during the great dispute between the Order and the Earl of Warenne.  In 1200 Lewes was without a Prior, and Abbot Hugh appointed one Alexander.  For some reason or other De Warenne refused to accept him and even went so far as to claim that the appointment lay with him, an impossible pretension.  Yet even within the Priory he is said to have won support, certain of the monks claiming that, save for a tribute of one hundred shillings a year to Cluny, they were independent.  The Pope was appealed to and he of course gave a clear decision, not in the English way of compromise, which is the way of a barbarian and a coward, but like an honest man deciding ’twixt right and wrong.  His judgment was wholly in favour of the Abbot of Cluny.  The Earl then began to bluster and to attempt to appeal beyond the Pope; he even dared to place armed men at the Priory gate and to stop all communications with Cluny.  The Abbot replied by an interdict upon Lewes, and things were in this confusion when the Pope appointed the Archbishop of Canterbury and the Bishops of Chichester and Ely to hear what De Warenne had to say in excuse for his violence.  The Abbot of Cluny himself came over and was insulted in Lewes by De Warenne’s men.  In appointing English judges to hear the case the Pope must have known that all would end in a compromise.  At any rate this is what happened, and it was decided that in future, when a vacancy occurred, the Abbot of Cluny should nominate two candidates of whom De Warenne should choose one for Prior.  This ridiculous judgment decided nothing.  Of two things, one; either the Abbot was right or he was wrong.  If he were right why should he forego his claim, to satisfy De Warenne who was wrong?  A decision was what was needed.  In 1229 the Pope rightly declared the compromise null and void, and the Abbot of Cluny regained his rights.  At once the moral condition of the house improved, and when it was visited in 1262 everything was reported to be satisfactory, and unlike any other Cluniac house in England this of Lewes was not in debt.

The turning point in the history of the Priory would seem to have been the one great moment in the story of the town; the appalling affair in which it was involved by Simon de Montfort in 1264 when he took the town, then Henry III.’s headquarters, and captured the King and young Prince Edward.  It would seem that De Montfort’s soldiers had very little respect for holy places, for we read that not only were the altars defiled but the very church was fired and hardly saved from destruction.

The quarrel between the King and his barons would seem, too, to have involved the monks, for we find the sub-prior and nine brethren were expelled from Lewes for conspiracy and faction and went to do penance in various houses of the Congregation.  Indeed such was the general collapse here that before the end of the century the Priory was practically bankrupt.