Organic agriculture requires farmers with the ability to develop profitable agro-enterprises on their own. By drawing on four years of experiences with the Enabling Rural Innovation approach in Uganda, we outline how smallholder farmers transition to organic agriculture and, at the same time, increase their entrepreneurial skills and competences through learning. In order to document this learning we operationalised the Kirkpatrick learning evaluation model, which subsequently informed the collection of qualitative data in two study sites. Our analysis suggests that the Enabling Rural Innovation approach helps farmers to develop essential capabilities for identifying organic markets and new organic commodities, for testing these organic commodities under varying organic farm management scenarios, and for negotiating contracts with organic traders. We also observed several obstacles that confront farmers’ transition to organic agriculture when using the Enabling Rural Innovation approach. These include the long duration of agronomic experimentation and seed multiplication, expensive organic certification procedures and the absence of adequate mechanism for farmers to access crop finance services. Despite prevailing obstacles we conclude that the Enabling Rural Innovation approach provides a starting point for farmers to develop entrepreneurial competences and profitable agro-enterprises on their own.