High quality, representative data from HIV surveillance systems that have country ownership and commitment are critical for guiding national HIV responses, especially among key and priority populations given their disproportionate role in the transmission of the virus. Between 2011 to 2013, the Mozambique Ministry of Health has conducted five Biobehavioral Surveillance Surveys among key populations (female sex workers, men who has sex with men and people who inject drugs) and priority populations (long distance truck drives and miners) as part of the national HIV surveillance system. We describe the experience of strengthening the HIV surveillance system among those populations through the implementation of these surveys in Mozambique. We document the lessons learned through the impact on coordination and collaboration; workforce development and institutional capacity building; data use and dissemination; advocacy and policy impact; financial sustainability and community impact. Key lessons learned include the importance of multisectoral collaboration, vital role of data to support key populations visibility and advocacy efforts, and institutional capacity building of government agencies and key populations organizations. Given that traditional surveillance methodologies from routine data often do not capture these hidden populations, it will be important to ensure that Biobehavioral Surveillance Surveys are an integral part of ongoing HIV surveillance activities in Mozambique.