This paper addresses the logistical challenges of implementing public health interventions in the setting of cluster randomized trials (CRTs), drawing on the experience of carrying out a CRT within a community-based health insurance (CBHI) scheme in rural India. Our CRT is seeking to improve the equity impact – i.e., reduce the differential in claims submission for hospitalization between poor and less poor – of this CBHI in rural areas. Five main challenges are identified and discussed: 1) assigning control clusters, 2) blinding, 3) implementing interventions simultaneously, 4) minimizing leakage, and 5) piggy-backing on a changing scheme. These challenges are not likely to be unique to low-income settings, although the fifth challenge is particularly likely when working with relatively small and resource-constrained programs. While compromises to methodological best-practice may reduce internal validity, they make the intervention more ‘real’, and potentially more applicable, to other programs and settings. Further, careful documentation of compromises allows them to be considered in the final analysis.