Background While greater reliance on nurse practitioners in primary healthcare settings can improve service efficiency and accessibility, their integration is not straightforward, challenging existing role definitions of both registered nurses and physicians. Developing adequate support practices is therefore essential in primary healthcare nurse practitioners’ integration. This study’s main objective is to examine different structures and mechanisms put in place to support the development of primary healthcare nurse practitioner’s practice in different healthcare settings, and develop a practical model for identifying and planning adequate support practices. Methods This study is part of a larger multicentre study on primary healthcare nurse practitioners in the province of Quebec, Canada. It focuses on three healthcare settings into which one or more primary healthcare nurse practitioners have been integrated. Case studies have been selected to cover a maximum of variations in terms of location, organizational setting, and stages of primary healthcare nurse practitioner integration. Findings are based on the analysis of available documentation in each primary healthcare setting and on semi-structured interviews with key actors in each clinical team. Data were analyzed following thematic and cross-sectional analysis approaches. Results This article identifies three types of support practices: clinical, team, and systemic. This three-level analysis demonstrates that, on the ground, primary healthcare nurse practitioner integration is essentially a team-based, multilevel endeavour. Despite the existence of a provincial implementation plan, the three settings adopted very different implementation structures and practices, and different actors were involved at each of the three levels. The results also indicated that nursing departments played a decisive role at all three levels. Conclusions Based on these findings, we suggest that support practices should be adapted to each organization’s environment and experience and be modified as needed throughout the integration process. We also stress the importance of combining this approach with a strong coordination mechanism involving managers who have in-depth understanding of nursing professional roles and scopes of practice. Making primary healthcare nurse practitioner integration frameworks more flexible and clarifying and strengthening the role of senior nursing managers could be the key to successful integration. Electronic supplementary material The online version of this article (doi:10.1186/s12913-017-2363-4) contains supplementary material, which is available to authorized users.