Sexual conflict develops when the optimal reproductive strategy for one sex inflicts fitness costs upon the other sex. Among species with intense within-group feeding competition and high costs of reproduction, females are expected to experience reduced foraging efficiency by associating with males, and this may compromise their reproductive ability. Here, we test this hypothesis in chimpanzees, a species with flexible grouping patterns in which female avoidance of large subgroups has been attributed to their relatively high costs of grouping. In an >11-year study of the Kanyawara community of East African chimpanzees (Pan troglodytes schweinfurthii) in the Kibale National Park, Uganda, the availability of sexually receptive females was a key determinant of the number of males in parties. In turn, females experienced significantly lower C-peptide of insulin levels, indicative of reduced energy balance, during periods when they associated with more males. Female associates did not produce the same negative effect. C-peptide levels positively and significantly predicted female ovarian steroid production, indicating that the costs of associating with males can lead to downstream reproductive costs. Therefore, we conclude that Kanyawara chimpanzees exhibit sexual conflict over subgroup formation, with the large groupings that allow males to compete for mating opportunities inflicting energetic and reproductive costs on females. Because association with males is central to female chimpanzees’ anti-infanticide strategy, and males may confer other benefits, we propose that reproductive success in female chimpanzees hinges on a delicate balance between the costs and benefits of associating with male conspecifics.