Community-based health promotion requires effective participation and partnership of diverse and numerous stakeholders from community as well as external professional organizations. Although effective partnership of stakeholders is often the key for success of health promotion practice and research, but this has proved to be a complex and challenging task. This study is an exploratory study to identify professional stakeholder's perspectives and experiences toward the partner's engagement challenges in community-based participatory research conducted in Population Research Centers in Iran. A qualitative study design with in-depth semi-structured interviews as data collection method was chosen. Using purposeful sampling technique, policy-makers and managers (mainly academics) involved in community-based participatory research in these centers were invited to be interviewed. Data were collected to the point where no new information was forthcoming. All interviews were taped and transcribed. To provide answers for research questions, qualitative content analysis was employed to extract emerging main themes from numerous cods. Findings were categorized in three main themes as Partnership's relationship and trust issues, Partnership's individual issues and Partnership's system issues. Although community-based participatory research in Iran benefits from more than a decade history and some physical infrastructures, but it seems that public health experts and researchers and other partner organizations are lagging behind in terms of capacities and competencies required to effectively utilize the available structure and opportunities. Hence, capacity development, both among professional partners and community may be the main way forward to tackling the future challenges for strengthening community actions but should include both levels of individuals and systems.