To study genetic effects of habitat fragmentation on plant performance and plant response to biotic interactions, we performed a greenhouse study with plants from 27 populations of the common plant Lychnis flos-cuculi differing in size, isolation, and microsatellite heterozygosity. We germinated seeds of 449 plants and grew up to nine offspring per maternal plant in single pots assigned to a factorial competition-by-pathogen infection treatment. We applied competition by sowing seeds of the grass Anthoxanthum odoratum into half of the pots. Moreover, half of the plants were inoculated with infective sporidia of the anther smut Microbotryum violaceum. Significant variation among populations in most size measures indicated genetic differentiation between populations. Plants from smaller populations developed fewer flowers than plants from larger populations indicating a genetic Allee effect. A decrease in flower number was also observed for populations with decreased microsatellite heterozygosity, suggesting higher inbreeding depression. Competition and pathogen infection reduced plant size independently from one another and independent from the fragmentation of the habitats of plant origin. While pathogen infection increased the total number of flowers per plant, it decreased the number of uninfected flowers per plant. This study demonstrates that even common species are negatively affected by habitat fragmentation. At the same time, it suggests little effect of habitat fragmentation on plant response to experimental competition and pathogen infection.