On 14 July 2013, Allen guided Limerick to a first Munster final appearance in six years, with his own native Cork providing the opposition. An even first half culminated with Cork's Patrick Horgan receiving a red card for striking Limerick wing-back Paudie O'Brien on the helmet under a high ball. Limerick took complete control in the second half and powered to a 0–24 to 0–15 victory. While Limerick were subsequently seen as favourites to land the All-Ireland crown, their championship campaign came to an end following an All-Ireland semi-final defeat by Clare.