Collaborative governance between public and civil society organizations (CSOs) in planning, managing, and providing welfare activities through horizontal organizing and equal relationships is described as necessary for addressing complex social problems. Synergies are expected when public organizations’ and CSOs’ different rationalities and goals are intertwined. However, theoretical frameworks illustrate collaboration as a dynamic process often involving conflicts. More studies are needed to explore the collaboration dynamics over time, investigating the conflicts that arise and how stakeholders handle them. This issue is addressed here through a cross-case analysis of four collaborative governance arrangements concerning welfare activities in Sweden, based on 63 semi-structured interviews, observations, and supplementary data. The results illustrate that more equal relationships were possible in three cases during the initial collaboration phase. However, demands from top-level municipal management for increased bureaucratization resulted in changes over time concerning defining the focus of collaboration and governance structure. To maintain influence, the CSOs used the strategies of adaptation, distancing, or exiting while the municipalities shifted from acting as partners to taking the ‘lead’. As a result, the CSOs’ influence diminished over time. Although the stakeholders’ differences motivate collaboration, these differences become problematic over time as the different perspectives fail to intertwine in an equal relationship when the projects’ activities are scaled up or linked to ordinary municipal operations. The marginalization of CSOs’ perspectives is problematic since collaboration, even in later phases, needs to be understood as dynamic, where CSOs’ perspectives are valuable for addressing complex social problems. The marginalization of CSOs in collaboration thus undermines both the idea of collaboration as an equal relationship and the possibility of addressing complex social problems through the intertwining of different perspectives.