AIDS Education and Prevention 22(5): 387-401 Community-based organizations (CBOs) play an important role in health promotion efforts and the delivery of HIV prevention interventions for at-risk minority populations. CBOs may also develop their own interventions but often lack the capacity or funds to rigorously evaluate them. The Innovative Interventions project of the Centers for Disease Control and Prevention (CDC) funded three CBOs to rigorously evaluate the efficacy of interventions they had developed and were delivering to Black women, Black men who have sex with men (MSM), and adolescent males in juvenile justice settings, respectively. The evaluation results have been reported elsewhere. This article describes operational issues that the CBOs identified as being particularly salient to their evaluations and the strategies they developed to address the issues and successfully complete their evaluations. These issues included the development of organizational capacity to conduct a rigorous outcome evaluation, difficulties with recruitment and retention of evaluation participants, and the use of process monitoring data to improve intervention delivery. The strategies described in this article can be used by CBOs when evaluating their locally developed HIV prevention interventions and may be of interest to funding agencies and researchers that collaborate with CBOs to evaluate their interventions.