Bacteria may colonize avian nests with unknown repercussions on nestling growth and health, although bacteria on nest materials may easily colonize nestling skin and growing feathers. Cavity nesters may have to build their nests on top of used nest materials, given restrictions on cavity availability. Nest reuse may favour bacterial colonization of nest materials and nestling skin and thereby affect nestling feather growth. To test these possibilities, we conducted a study of Pied Flycatchers Ficedula hypoleuca breeding in nest-boxes in central Spain. We left a sample of nest-boxes without removing old nest materials in 2010 and compared bacterial loads of nest materials, control inert objects and nestling belly skin in reused nests with those in new nests in 2011. Nestlings raised in reused nests had higher bacterial loads on their belly skin than those in new nests, while no difference between nest types for nest materials and control inert objects were found. There was a marginally significant tendency for wing length before fledging to be lower in reused nests, but no trend for mass or tarsus length. The bacterial loads of nests showed a negative association with feather growth of nestlings as expressed through wing length but not with tarsus length or mass growth. These results indicate an association between nest reuse and bacterial growth on nestling skin not hitherto detected. They also suggest a possible impairment of flight capacity at fledging mediated by nest bacterial communities which are in direct contact with nestling skin and growing feathers.