Background Community empowerment initiatives are receiving increased interest as ways of improving health and reducing health inequalities. Purpose Longitudinally examine associations between collective control, social-cohesion and mental wellbeing amongst participants in the Big Local community empowerment initiative across 150 disadvantaged areas of England. Methods As part of the independent Communities in Control study, we analysed nested cohort survey data on mental wellbeing (Short Warwick Edinburgh Mental Wellbeing Scale—SWEMWBS) and perceptions of collective control and social-cohesion. Data were obtained in 2016, 2018 and 2020 for 217 residents involved in the 150 Big Local areas in England. Adjusted linear mixed effect models were utilized to examine changes in SWEMWBS over the three waves. Subgroup analysis by gender and educational level was conducted. Results There was a significant 1.46 (0.14, 2.77) unit increase in mental wellbeing score at wave 2 (2018) but not in wave 3 (2020) (0.06 [−1.41, 1.53]). Across all waves, collective control was associated with a significantly higher mental wellbeing score (3.36 [1.51, 5.21]) as was social cohesion (1.09 [0.19, 2.00]). Higher educated participants (1.99 [0.14, 3.84]) and men (2.41 [0.55, 4.28]) experienced significant increases in mental wellbeing in 2018, but lower educated participants and women did not. Conclusion Collective control and social cohesion are associated with better mental wellbeing amongst residents engaged with the Big Local initiative. These health benefits were greater amongst men and participants from higher educational backgrounds. This suggests that additional care must be taken in future interventions to ensure that benefits are distributed equally.