Sub-Saharan African countries, through their regional organizations, have embarked on the harmonisation of plant variety protection (PVP) systems. These initiatives are largely modelled on the UPOV 1991 act, which claims to incentivize plant breeding and facilitate agricultural development. Civil Society Organisations (CSO), however, strongly criticise this process for being out of step with Sub-Saharan African agricultural realities, undermining smallholder farmers’ agricultural practices and, ultimately, threatening food security. Among their main concerns are the fear that the proposed regimes facilitate biopiracy and lack recognition of farmers’ rights. This article discussed three of the main CSO concerns in tandem with examples of alternative provisions from PVP systems from around the world. While it will be shown that the CSO concerns are not likely to be acted upon, this article aims to answer the pressing question whether a UPOV ’91 based PVP system hampers farming practices in developing countries, and explores several legal avenues to accommodate the needs and traditions of smallholder farmers.