Farmer-managed seed systems and the conservation of agrobiodiversity are increasingly recognized as important components of food and seed sovereignty. In contrast, hybrid, genetically modified (GM), and, increasingly, gene-edited crops continue to be promoted by Green Revolution proponents as a “climate smart” package that includes fertilizers, pesticides, purchased seeds, and links to global markets. Influencing seed laws and policies to support the uptake of modern crop varieties has been a key entry point in many countries, facilitated by networks of foreign donors, philanthropists, governments, and multinational companies. Using the case of South Africa, where GM crops have been grown for several decades, we provide insights on implications for Malawi, which passed a Seed Act in 2022, implicitly supporting GM crops. Both countries have histories of colonial agriculture with strong policy support for modern, hybrid varieties of maize, and the replacement (and displacement) of local, open-pollinated maize varieties. In South Africa, several studies have revealed the contamination of smallholder fields and seed systems. Through a political ecology lens, we explore how maize and its cotechnologies were commodified in South Africa and Malawi, and what South African experiences of GM crop adoption in smallholder farming systems can tell us about the challenges to be faced by smallholder Malawian farmers. We reveal how colonial histories and ongoing colonialities of power, knowledge, being, and nature continue to shape the character and form of agriculture in both countries, running counter to the needs of agroecological smallholder farmers and their ways of knowing and being. We conclude by envisioning what reimagined, transformed and decolonial approaches for food and agriculture might look like on the African continent, and how they might contribute toward the attainment of food and seed sovereignty and an agroecological future.