OBJECTIVE: Identify the programmatic barriers that hinder access to comprehensive care of patients with tuberculosis and human immunodeficiency virus (TB/HIV) coinfection. METHODS: This is a mixed-method study. Qualitative research was conducted via in-depth interviews with key actors and the quantitative component involved cross-sectional descriptive analysis of programmatic data from 2010-2015 on tuberculosis and HIV programs at health facilities in the cities of Lima and Iquitos. RESULTS: Twenty-two key actors in seven establishments were interviewed. The identified barriers were: little or no coordination between tuberculosis and HIV teams, separate management of tuberculosis and HIV cases at different levels of care, insufficient financing, limited or poorly trained human resources, and lack of an integrated information system. It was found that HIV screening in TB patients increased (from 18.8% in 2011 to 95.2% in 2015), isoniazid coverage of HIV patients declined (from 62% to 9%), and the proportion of deaths among TB/HIV coinfection cases averaged 20%. CONCLUSIONS: There is poor coordination between HIV and TB health strategies. Management of TB/HIV coinfection is fragmented into different levels of care, which has an impact on comprehensive patient care. As a result of this research, a technical document was prepared to establish joint procedures that should be implemented to improve comprehensive care of TB/HIV coinfection.