Multi-stakeholder platforms (MSPs) have been playing an increasing role in interventions aiming to generate and scale innovations in agricultural systems. However, the contribution of MSPs in achieving innovations and scaling has been varied, and many factors have been reported to be important for their performance. This paper aims to provide evidence on the contribution of MSPs to innovation and scaling by focusing on three developing country cases in Burundi, Democratic Republic of Congo, and Rwanda. Through social network analysis and logistic models, the paper studies the changes in the characteristics of multi-stakeholder innovation networks targeted by MSPs and identifies factors that play significant roles in triggering these changes. The results demonstrate that MSPs do not necessarily expand and decentralize innovation networks but can lead to contraction and centralization in the initial years of implementation. They show that some of the intended next users of interventions with MSPs–local-level actors–left the innovation networks, whereas the lead organization controlling resource allocation in the MSPs substantially increased its centrality. They also indicate that not all the factors of change in innovation networks are country specific. Initial conditions of innovation networks and funding provided by the MSPs are common factors explaining changes in innovation networks across countries and across different network functions. The study argues that investigating multi-stakeholder innovation network characteristics targeted by the MSP using a network approach in early implementation can contribute to better performance in generating and scaling innovations, and that funding can be an effective implementation tool in developing country contexts.