The amalgamation of the three schools in Cahersiveen in 1999 led to the creation of Coláiste na Sceilge. O'Connor remained on the teaching staff while also holding on to his position as coach of the school's football team. In 1999 he guided the school to another set of county and provincial vocational titles while another All-Ireland final appearance beckoned. Holy Trinity College provided the opposition on that occasion, however, victory went to the Kerry team. In 2000 Coláiste na Sceilge made history when they retained their county, Munster and All-Ireland vocational titles.