This article examines the role of innovation capacity and business process agility (BPA) in the relationship between supply chain collaboration (SCC) and supply chain performance (SCP) of smallholder agro-based enterprises (SAEs). Based on the relational view and dynamic capability theories and the survey research design, the author used questionnaires to gather data from 226 SAEs who were sampled from agribusiness associations in four regions of Ghana via the quota sampling technique. Smart PLS-SEM 4.0 was used as the statistical method to analyze the data. The results showed that SCC has a significant and positive relationship with SCP, innovation capacity, and BPA. Innovation capacity significantly mediates the relationship between SCC and SCP. Furthermore, BPA fully mediates the relationship between SCC and innovation capacity, with innovation capacity also influencing SCP. This study integrates relational and capability-based views to propose a comprehensive theoretical model showing the inter-relational effect of SCC, BPA, and innovation capacity on SCP. The empirical findings widen the context of SCC literature to include SAEs from emerging economies in sub-Saharan Africa. The empirical findings enrich the understanding of how SAEs can manage their SCCs to develop and use specific capabilities that positively impact SCP. The uniqueness of this article rests in the proposed model and new empirical knowledge, which extends the scope of the relational and capability-based views and SCC literature to include innovation capacity, BPA, and SCP of SAEs in emerging markets.