This article critically examines the agricultural development agenda of promoting commercialization and sustainable intensification and contrasts this with farmers’ own priorities, with case studies drawn from the maize and cocoa sectors in Ghana. The study investigates the relationship between agricultural development paradigms, seed breeding strategies, and the commercialization of agriculture from the 1950s to present. It returns to the debates of farming systems research, the appropriation of the agricultural varieties of farmers within the South by Northern agribusiness, and Paul Richards’ framework of an Indigenous African agricultural revolution rooted in the experimental traditions of farmers to establish a critical framework for examining the commodification of seeds. It focuses on the contradictions between maintaining biodiversity, fashioning high-yielding proprietary seeds, and promoting farmer participation that became manifest in the framework of farming systems research. It argues that commercial pressures have prioritized yields and the protection of proprietary varieties over biodiversity in policy frameworks. This contrast with farmers’ own concerns with adapting varieties to the conditions on their farms through their own experimentation, and maintaining a diversity of changing genetic materials including those drawn from certified varieties. This enables farmers to hedge against risk, disease, and pest attacks, while selecting varietal materials that optimize yields in the particular agroecological conditions of their farms. Although social participation is still upheld as an important value in liberal market agrarian policies, there has been a significant transformation in its usage. It no longer denotes farmer participation in the design of and experimentation with technology, but participation in the consumption of the agricultural products of agribusiness or in the agricultural technology treadmill. This contribution examines the implication of smallholder agricultural commercialization for biodiversity and for the dynamism and vitality of local farming systems.