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Purpose: To examine factors associated with adherence of patients on Anti-tuberculosis treatment in Health facilities at Masaka City. Specifically the study was guided by four objectives; to establish the current level of adherence, to explore the patient knowledge, to find out socio-economic factors, and to identify Health facility factors contributing to adherence of patient on tuberculosis treatment. Methodology: A cross-sectional research design with both quantitative and qualitative approaches of data collection and analysis was used. At least 110 patients on tuberculosis drug were selected and 15 health workers working in tuberculosis clinics to give expert views on the problem under investigation. Interview guide and questionnaires were used and data were analyzed using Stata version 13. Descriptive statistics, percentages were presented in the findings on frequency distribution tables. Qualitative data obtained using interviews was analyzed using thematic content analysis and narrative reasoning. Results: Prevalence of adherence to TB treatment was at 86% from the patients the study was conducted. In the study most patients had adequate knowledge on Tuberculosis treatment and it had attributed a majority 86% with good adherence on Tuberculosis Drug. On health facility factors there was limited medical supplies of drug to improve care, most patients were youth. Statistically, there was significant relationship between frequent counseling and patient adherence at multivariate levels. (OR=15.5073; [95% Cl: 3.73553 to 27.27917]; p=0.010). There was no relationship between patients’ adherence and employment status and good conduct of health workers was significally associated with patient adherence. (OR=7.0566; [95%Cl: 2.77620 to 11.3371]; P=0.001). In this study factors affecting adherence included stigma, discrimination and suspension of transport as COVID-19 prevention guideline by Ministry of health Uganda negatively contributed to poor adherence of patients. This was attributed to by isolation and neglect by family members, relatives, health workers and the community for fear of COVID-19 suspicion at each respective health facility. Involvement of TB survivor in TB treatment would increase adherence and retention in care. Recommendations: In the study there was suboptimal adherence of 86% as opposed to MOH Uganda of 95%, due to stigma and discrimination. The study recommended each TB patient be assigned a family member and a village health team as treatment supporters. Intensified health education and pre TB treatment counselling on adherence increases patients ability to take medication consistently leading to good TB treatment outcomes. Not involving and supporting private clinics to provide TB services is a very big missed opportunity by the health sector. Most patients first visit private clinics before coming to public health centers. Involvement of TB survivor in TB treatment would increase adherence and retention in care.