Peru has applied to six of the Global Fund to Fight AIDS, Tuberculosis and Malaria (the Global Fund) rounds for funding, achieving success on four occasions. The process of proposal development has, however, been criticised, especially concerning the use of evidence, relevance/consistency and performance indicators. We aimed to analyse the Peruvian Global Fund proposals according to those dimensions, providing feedback to improve future local efforts and inform global discussions around Global Fund procedures. We analysed the content of four HIV-focused proposals (rounds 2, 5, 6 and 8) regarding epidemic context, needs identification and prioritisation and monitoring and evaluation systems. Peruvian proposals submitted after round 1 were described as resulting from collaborative inputs involving formerly unrepresented sectors, principally 'vulnerable populations'. However, difficulties arose regarding the amount and quality of evidence about the epidemiological context; limited consideration of social determinants of the epidemic; lack of theory-driven interventions, and little synergy across projects and the inclusion of weak monitoring and evaluation systems, with poor indicators and measurement procedures. Prioritising the development of analytical and technical skills to generate Global Fund proposals would enhance the country's capacity to produce and utilise evidence, improve the technical-political interface, strengthen information systems and lead to more informed decision making and accountability. © 2013 Taylor & Francis.