Objective: In most African countries, primary care is delivered through a district health system. Many factors, including staffing levels, staff experience, availability of equipment and facility management, affect the quality of primary care between and within countries. The purpose of this study was to assess the quality of primary care in different types of public health facilities in Southern Malawi. Study design: This was a cross sectional quantitative study. Setting: The study was conducted in 12 public primary care facilities in Neno, Blantyre and Thyolo districts in July 2018. Participants: Patients aged 18 years and above, excluding the severely ill, were selected to participate in the study. Primary outcomes: We used the Malawian primary care assessment tool to conduct face-to-face interviews. ANOVA at 0.05 significance level was performed to compare primary care dimension means and total primary care scores. Linear regression models at 95% CI were used to assess associations between primary care dimension scores, patients’ characteristics and healthcare setting. Results: The final number of respondents was 962 representing 96.1% response rate. Patients in Neno hospitals scored 3.77 points higher than those in Thyolo health centers, and 2.87 higher than those in Blantyre health centers in total primary care performance. Primary care performance in health centers and in hospital clinics was similar in Neno (20.9 vs 19.0, p= 0.608) while in Thyolo, it was higher at the hospital than at the health centers (19.9 vs 15.2, p<0.001). Urban and rural facilities showed a similar pattern of performance. Conclusion: These results showed considerable variation in experiences among primary care users in the public health facilities in Malawi. Factors such as funding, policy and clinic level interventions influence patients’ reports of primary care performance. These factors should be further examined in longitudinal and experimental settings.