Introduction HIV-related internalized stigma remains a major contributor to challenges experienced when accessing and providing HIV diagnosis, care and treatment services. It is a key barrier to effective prevention, treatment and care programs. This study investigated experiences of internalized stigma among people living with HIV in Malawi. Methodology A participatory cross-sectional study design of participants from eight districts across the three administrative regions of Malawi. Data were collected using Key Informant Interviews (n = 22), Focus Group Discussions (n = 4) and life-stories (n = 10). NVIVO 12 software was used for coding applying both deductive and inductive techniques. Health Stigma and Discrimination Framework was used as a theoretical and analytical framework during data analysis. Results Overt forms of stigma and discrimination were more recognizable to people living with HIV while latent forms, including internalized stigma, remained less identifiable and with limited approaches for mitigation. In this context, manifest forms of HIV-related stigma intersected with latent forms of stigma as people living with HIV often experienced both forms of stigma concurrently. The youths, HIV mixed-status couples and individuals newly initiated on ART were more susceptible to internalized stigma due to their lack of coping mechanism, unavailability of mitigation structures, and lack of information. Broadly, people living with HIV found it difficult to identify and describe internalized stigma and this affected their ability to recognize it and determine an appropriate course of action to deal with it. Conclusion Understanding the experiences of internalized stigma is key to developing targeted and context specific innovative solutions to this health problem.