North–South research capacity building (RCB) partnerships have attracted considerable academic attention during the last two decades, especially with regard to issues related to partnership governance. Less attention has been given to the management aspects of partnership implementation, but in order for partnerships to comply with general governance-level recommendations, a better understanding is needed of how specific context-dependent factors influence the development and execution of projects. In this article, we aim to contribute to the understanding of factors influencing the design phase of RCB partnerships and examine how they influence the balance between performing collaborative research and developing general organizational capacity. Data collection was based on a survey (n = 25), and individual interviews and focus group discussions with 17 Danish project managers from the Danish Bilateral Programme for Enhancement of Research Capacity in Developing Countries. Our results lead to rejection of the proposition that RCB projects are either focused on building capacity for research or conducting merit-based research. Because of the ‘politics’ of the front-end process, reality is more complex. We identify 11 specific factors influencing front-end project management related to structure, process and relationship, and we theorize about how these factors influence the choice between research and more general capacity development activities. Copyright © 2013 John Wiley & Sons, Ltd.