Vaccination against COVID-19 remains one of the ultimate solutions to the ongoing pandemic. This study examined and compared the completion of primary COVID-19 vaccination series and associated factors in the slum and estate communities of Uganda. This was a cross-sectional survey conducted among 1025 slum and estate residents. Logistic regression models were fitted. Of the 1025 participants, 511 were slum residents and 514 were estate residents. Completion of COVID-19 vaccination was 43.8% in the slum community and 39.9% in the estate community (p = 0.03). Having more knowledge about COVID-19 was positively associated with completing COVID-19 vaccination in both communities. Perceived benefits and cues to action also had a positive association, but only among the slum residents. However, perceiving people infected with COVID-19 as having a high death rate, perceived barriers such as serious side effects and long distances, and depressive symptoms had negative associations with vaccine uptake among the slum community, but not in the estate community. Addressing barriers to vaccination, strengthening and utilizing the various cues to action, engagement of religious and cultural leaders, and continued community education and sensitization tailored to the needs of each community are potentially vital strategies in raising vaccination rates. Consideration of socioeconomic impact-alleviation strategies, especially among the urban poor, would also be beneficial.