The College was intended by Bishop Fleming to train clergy to confute the prevalent Lollard heresy, a precursor of the Protestant movement that was later to result in the Reformation. He had once been thought, unjustifiably, to sympathise with Lollard teaching, and had become one of its leading opponents. He designed the new society as a 'little college of true students of theology who would defend the mysteries of Scripture against those ignorant laymen who profaned with swinish snouts its most holy pearls'.
Accordingly, he obtained from King Henry VI a charter (13 October 1427) to unite the three parishes of All Saints', St Michael's and St Mildred's, into a college consisting of a Warden or Rector and seven Fellows, who were to study theology, 'the empress and mistress of all the faculties', and to pray for the welfare of the founder during his life and for the health of his soul after his death.
Its early days were very precarious. Fleming died in 1431 and it was only with the assistance of substantial benefactions from others, notably John Forrest, Dean of Wells, that the main quadrangle complete with Chapel, Library, Hall and Kitchen was constructed during the following decades. Among other benefactors were Emily Carr and her husband, who gave the College Nos 113 and 114 High Street with land stretching back to Bear Lane. These properties remain in the possession of the College and in the last decades of the twentieth century, six hundred years after Emily Carr's death, have enabled it to extend its student accommodation and other facilities across the High Street to run as far as the walls of Christ Church.
The fifteenth-century civil wars between the Houses of York and Lancaster, the 'Wars of the Roses', posed a considerable threat to Lincoln, whose founding charter had been obtained from the deposed Lancastrian king, Henry VI. It took strenuous efforts by friends of the College to obtain recognition of its legality by the Yorkist kings. Instrumental in this process was the Visitor, Bishop Thomas Rotherham of Lincoln, who visited the College in 1474 and was inspired by a sermon preached by the Rector on the text 'Behold and visit this vine, and complete that which thy right hand hath planted' (Psalm LXXX80, 14-15). The occasion and Rotherham's undertaking to complete the foundation of the College are commemorated to this day by a vine which grows in the College (now in Chapel Quadrangle). The Charter which Rotherham obtained from Edward IV in 1478 effectively made the bishop the second founder of the College. The code of statutes which he issued in 1480 remained in force until the Royal Commission of 1854.