Abstract Background The systematic involvement of project beneficiaries in community maternal and child health programmes remains low and limited, especially during the formative stages of the project cycle. Understanding how positive and negative feedbacks obtained from communities can subsequently be used to inform and iterate existing programmes is an important step towards ensuring the success of community health workers for maternal and child health programming and, ultimately, for improving health outcomes. Methods The study took place over a period of 4 weeks in North Rukiga, Kabale District of southwestern Uganda. Using a cross-sectional qualitative study that employed an epistemological approach of phenomenology, nine focus group discussions and eight in-depth interviews were conducted with a total of 76 female participants across six different sites. Women were identified as either users or non-users of the maternal and child health programme. Purposeful sampling was employed to recruit women from six different locations within the programme catchment area. Translated and transcribed transcripts were subjected to a bottom-up thematic analysis using NVivo 10 Software, whereby themes were arrived at inductively. Results Predominant themes emerging from the focus groups and key informant interviews identified early trends in programme strengths. Beneficiaries reported confidence in both the programme and the relationships they had forged with community health workers, exhibited pride in the knowledge they had received, and described improved spousal involvement. Beneficiaries also identified a number of programme challenges including barriers to adopting the behaviours promoted by the programme, and highlighted issues with programme dependency and perceived ownership. It also emerged that community health workers were not reaching the entire population of intended programme beneficiaries. Conclusions This research provides support for the importance of an early-stage participatory evaluation of beneficiaries’ perceptions of newly initiated health programmes. Our results support how evaluations conducted in the early phases of programme implementation can provide valuable, timely feedback as well as yield recommendations for programme adjustment or re-alignment, and in turn, better meet end-user expectations. Potential reasons for the observed lack of community participation in early stages of programme implementation are considered.