Extra-pair paternity (EPP) in socially monogamous species has been associated with the genetic benefits incurred by females through extra-pair mate choice. There is conflicting evidence in the literature concerning the importance of such benefits possibly due to their context-dependence. To ascertain if there are such context-dependent genetic benefits, we conducted a brood manipulation experiment in pied flycatchers (Ficedula hypoleuca) breeding in central Spain. We found that extra-pair mates (EPM) are frequently not nearest neighbours. Cuckolded males and EPM did not differ from other males in any measured trait, and were not different either when cuckolds and cuckolders were compared within broods. Within-pair offspring (WPO) and extra-pair offspring (EPO) did not differ with respect to heterozygosity and no association of heterozygosity of either offspring or males and females with EPP could be detected. Moreover, the competitive context in the nest induced by brood manipulations affected the growth of nestlings and showed an interaction with paternity differences in nestling mass but in the opposite direction to the prediction of context-dependence, i.e., EPO were lighter than WPO in enlarged broods but not in control broods. Furthermore, EPO had shorter tarsi than WPO in all treatments. Mortality in the nest showed an association with brood manipulation treatment, but not with paternity or its interaction with treatment. Thus, we have not found any evidence of genetic benefits, context-dependent or otherwise, of EPP in our study population. The evidence of poor quality EPO does not support a mixed reproductive strategy of females in our population.