Purpose Exercise program preferences are important for designing physical activity (PA) interventions; yet may change following an intervention. Further, the relationship between preferences and PA behavior change is unclear. This study evaluated exercise program preferences among breast cancer survivors (BCS) before and after a behavioral intervention and associations between program preferences and PA change. Methods BCS were randomized to the BEAT Cancer intervention (n = 110) or written materials (n = 112). Questionnaires assessed exercise program preferences. Minutes per week of moderate-to-vigorous PA (MVPA) were accelerometer-measured and self-reported at baseline (M0), post-intervention (M3), and 3-month follow-up (M6). Results At M0, the majority of intervention group participants preferred exercising with others (62%) yet shifted to preferring exercising alone (59%) at M3 ( p < 0.001). Furthermore, preferring exercising with others at M0 was associated with greater increases in self-reported MVPA between M0 and M6 (124.2 ± 152 vs. 53.1 ± 113.8, p = 0.014). BCS preferring facility-based exercise decreased after the BEAT Cancer intervention (14% vs. 7%, p = 0.039) and preferring exercising at home/had no preference at M0 had greater improvements in accelerometer-measured MVPA from M0 to M3 (74.3 ± 118.8 vs. -2.3 ± 78.4, p = 0.033) and M0 to M6 (44.9 ± 112.8 vs. 9.3 ± 30.4, p = 0.021). Exercise program preferences regarding mode of counseling, training supervision, and type of exercise changed from M0 to M3 but were not associated with changes in MVPA. Conclusion Findings suggest BCS exercise program preferences may change after an intervention and be associated with changes in MVPA. Understanding the role of PA preferences will better inform the design and success of PA behavior change interventions. ClinicTrials.gov, ClinicalTrials.gov number: NCT00929617.