Objectives Female bonobos (Pan paniscus) are characterized as highly affiliative and cooperative, but few studies have quantified the strength and stability of female intra‐sexual relationships or explored how variation in social relationships influences cooperation. We measure female social preferences, identify causes of variation in preferences, and test whether variation in social preferences predicts food sharing or coalitionary support. Methods Data were collected over 3 years from females in the Bompusa community at LuiKotale, DRC. We measured genetic relatedness and constructed social preference indices for party association, proximity, grooming, GG‐rubbing and aggression. We identified preferred social partners based on permutation tests and measured stability using Mantel tests. We used factor analysis to identify inter‐relationships between preference indices and used LMMs to test whether variation in social preferences was explained by relatedness, rank differences, having dependent young or co‐residency time. We used GLMMs to test whether variation in social preferences predicted food sharing or coalitionary support. Results All females had preferred non‐kin partners for proximity, grooming or GG‐rubbing, but only grooming preferences were stable across years. Association indices were higher among lactating females, and aggression was lower among females with longer co‐residency times. The factor analysis identified one factor, representing proximity and GG‐rubbing preferences, labeled behavioral coordination. Dyads with higher levels of behavioral coordination were more likely to share food. Conclusions Female bonobos exhibit stable, differentiated grooming relationships outside of kinship and philopatry. Females also exhibit flexible proximity and GG‐rubbing preferences that may facilitate cooperation with a wider range of social partners.