South African democratic governments instituted several policies aimed at developing the capabilities of smallholder foresters to ensure economic inclusion and rural development. Skills development to build smallholder capabilities was deemed necessary to improve productivity, food security and conserve forestry resources. However, systemic blockages within the South African skills system hinder skills development, knowledge and technological flows to smallholders. This study assessed the systemic blockages hindering forestry skills formation and knowledge flows in the South African provinces of Mpumalanga and KwaZulu-Natal. In-depth interviews were conducted with policy practitioners, skills researchers, forestry organisations, and smallholder foresters. The interviews covered issues about alignment in government departments, extension curricula, linkages and interactions between skills institutions, extension officers and smallholders and other economic agents. Thematic analysis established that systemic blockages within the South African skills systems emanate from the lack of policy implementation resulting from the misalignment in government departments. Weak linkages and interactions between policymakers, researchers, extension officers and smallholders and traditional institutions also limit interactions, sharing and co-generation of skills and knowledge for application by smallholders. This paper recommends monitoring mechanisms to ensure interactive and coordinated implementation of forestry and innovation policies for knowledge to flow to smallholders.