HIV clinical mentoring has been utilized for capacity building in Africa, but few formal program evaluations have explored mentee perspectives on these programs. EQUIP is a PEPFAR-USAID funded program in Malawi that has been providing HIV mentoring on clinical and health systems since 2010. We sought to understand the successes and challenges of EQUIP's mentorship program. From June-September 2014 we performed semi-structured, in-depth interviews with EQUIP mentees who had received mentoring for ≥ 1 year. Interview questions focused on program successes and challenges and were performed in English, audio recorded, coded, and analyzed using inductive content analysis with ATLAS.ti v7. Fifty-two mentees from 32 health centers were interviewed. The majority of mentees were 18-40 years old (79%, N = 41), 69% (N = 36) were male, 50% (N = 26) were nurses, 29% (N = 15) medical assistants, and 21% (N = 11) clinical officers. All mentees felt that EQUIP mentorship was successful (100%, N = 52). The most common benefit reported was an increase in clinical knowledge allowing for initiation of antiretroviral therapy (33%, N = 17). One-third of mentees (N = 17) reported increased clinic efficiency and improved systems for patient care due to EQUIP's systems mentoring including documentation, supply chain and support for minor construction at clinics. The most common challenge (52%, N = 27) was understaffing at facilities, with mentees having multiple responsibilities during mentorship visits resulting in impaired ability to focus on learning. Mentees also reported that medication stock-outs (42%, N = 22) created challenges for the mentoring process. EQUIP's systems-based mentorship and infrastructure improvements allowed for an optimized environment for clinical training. Shortages of health workers at sites pose a challenge for mentoring programs because mentees are pulled from learning experiences to perform non-HIV-related clinic duties. Evaluations of existing mentoring models are needed to continue to improve mentoring strategies that result in sustainable benefits for mentees, facilities, and patients.