A visible light photocatalytic metal-free perfluoroalkylation method for the functionalization of heteroarenes in continuous flow was developed. Eosin Y was the most efficient photocatalyst with regard to substrate scope, reaction time and cost prize. Faster reaction times were observed in continuous flow compared to batch due to an improved irradiation of the reaction mixture on a microscale. Several pyrroles and indoles were perfluoroalkylated within 30 min residence time (six examples). The trifluoromethylation of pyrroles and indoles was achieved by using a gas–liquid flow with CF3I as a cheap CF3 source (three examples).