Innovation, accompanied by structural change, is at the heart of economic growth and development. Yet there is limited evidence to understand interactions between innovation, structural change and inclusion in the context of low-income and emerging countries, or how these processes best support sustainable and inclusive societies. Through case studies of innovation pathways in breeding practices in the Kenyan dairy sector and anti-retroviral therapy service provision in Mozambique, we study how innovations in specific contexts lead to adoption, diffusion and upgrading, and further to structural change and inclusion or exclusion of marginalised groups. The case studies unpack the conditions for these outcomes by identifying key variables, actors and interactions that shape the innovation pathways. We find that capabilities is a key variable. In particular, we find that inclusiveness and structural changes impact successive phases of innovations through ‘reinforcing’ or ‘balancing mechanisms’, operationalised by the impact of innovation on capabilities. Other factors include the presence of interrelated innovations, power relations between actors, and the role of institutions (formal and informal). The Kenyan case suggests parallel non-competing innovation pathways, while for Mozambique, we observe competing pathways that remain to be examined further. Findings from the cases provide the basis of future primary research on inclusive structural change.