This study investigated the effect of mental disorders on the mental wellbeing of prisoners in selected prisons in Kenya. A mixed method study design was employed in which quantitative and qualitative data was collected concurrently. A sample of 364 respondents was obtained using multistage sampling technique. The study used a structured questionnaire, Warwick-Edinburg Mental Wellbeing Scale (WEMWBS), MINI International Neuropsychiatric Interview, FGD and Key Informant Interview Schedules. Descriptive and inferential statistics were used to analyze quantitative data while thematic analysis was used to analyze qualitative data. The ANOVA test results indicated that mental disorders affect mental wellbeing of prisoners (p-value <0.0001). Suicidality, panic disorder, PTSD and mood disorder with psychotic features were significantly associated with mental wellbeing at p=0.001, p=0.015, p=0.044 and p=0.019 respectively. The Kenya Prison Service management needs to establish comprehensive mental health services at all prisons as provided for in the Prisons Act for achievement of better mental wellbeing of prisoners.