Background Training of health professionals can be deliberately structured to enhance rural recruitment by exposing the trainees to the realities of rural life and practice through Community-Based Education and Service (COBE) programs. Few studies have surveyed the alumni of these programs to establish their post-university views and whether the positive impact of COBE programs endures into the post-university life. This study surveyed the alumni of COBE at Makerere to obtain their perceptions of the management and administration of COBE and whether COBE had helped develop their confidence as health workers, competence in primary health care and willingness and ability to work in rural communities. Objectives To assess the efficiency of the management and administration of COBES. To obtain the views of the impact of COBES on its alumni. Methods A mixed qualitative and quantitative study was conducted using focus group discussions (FGD) and a telephone administered questionnaire. From a total of 300 COBES alumni 150 were contacted. Twenty four Alumni (13 females and 11 males) were purposefully selected by discipline, gender and place of work, and invited for the focus group discussion. The discussions were transcribed and analyzed using a manifest content analysis table. The thematic issues from the FGDs were used to develop a structured questionnaire which was administered by telephone by the authors. The data were entered into Microsoft excel template and exported to Stata for analysis. The findings of the telephone survey were used to cross-match the views expressed during the focus group discussions. Results The alumni almost unanimously agree that the initial three years of COBES were very successful in terms of administration and coordination. COBES was credited for contributing to development of confidence as health workers, team work, communication skills, competence in primary health care and willingness to work in rural areas. The COBES alumni also identified various challenges associated with administration and coordination of COBES at Makerere. Conclusions This study has established that the positive impact of COBES endures with the alumni of the program. Health planners should take advantage of the impact of COBES and provide it with more support.