Policy makers throughout the world are struggling to find effective ways to prevent the rising trend of obesity globally, particularly among children. The Pacific Obesity Prevention in Communities project was the first large-scale, intervention research project conducted in the Pacific aiming to prevent obesity in adolescents. The project spanned four countries: Australia, New Zealand, Fiji and Tonga. This paper reports on the strengths and challenges experienced from this complex study implemented from 2004 to 2009 across eight cultural groups in different community settings. The key strengths of the project were its holistic collaborative approach, participatory processes and capacity building. The challenges inherent in such a large complex project were underestimated during the project's development. These related to the scale, complexity, duration, low research capacity in some sites and overall coordination across four different countries. Our experiences included the need for a longer lead-in time prior to intervention for training and up-skilling of staff in Fiji and Tonga, investment in overall coordination, data quality management across all sites and the need for realistic capacity building requirements for research staff. The enhanced research capacity and skills across all sites include the development and strengthening of research centres, knowledge translation and new obesity prevention projects.