Peru has received around $70 million from Global Fund to fight AIDS, Tuberculosis and Malaria (Global Fund). Recent economic growth resulted in grant ineligibility, enabling greater government funding, yet doubts remain concerning programme continuity. This study examines the transition from Global Fund support to increasing national HIV/AIDS funding in Peru (2004–2012) by analysing actor roles, motivations and effects on policies, identifying recommendations to inform decision-makers on priority areas. A conceptual framework, which informed data collection, was developed. Thirty-five in-depth interviews were conducted from October to December 2011 in Lima, Peru, among key stakeholders involved in HIV/AIDS work. Findings show that Global Fund involvement led to important breakthroughs in the HIV/AIDS response, primarily concerning treatment access, focus on vulnerable populations and development of a coordination body. Nevertheless, reliance on Global Fund financing for prevention activities via non-governmental organisations, compounded by lack of government direction and weak regional governance, diluted power and caused role uncertainty. Strengthening government and regional capacity and fostering accountability mechanisms will facilitate an effective transition to government-led financing. Only then can achievements gained from the Global Fund presence be maintained, providing lessons for countries seeking to sustain programmes following donor exit.