Through a European Union funded project called JOLISAA (Joint Learning in Innovation Systems in African Agriculture), the nature of smallholder oriented innovation systems have been explored in terms of partnerships, triggers that have given rise to them and the nature of the innovations themselves. The main objective was to analyse a broad diversity of multi-stakeholder agricultural innovation processes involving smallholders. The analysis of 11 cases documented comprises innovation bundles composed of technical, organisational and institutional innovations. The eleven cases documented showed that six exhibited non-technical innovation processes frequently related to market access as well as to inputs and services. Triggers that drive smallholders and other stakeholders to initiate innovation processes include environment stress, introduction of new technologies, identification of market change as well as policy or regulatory changes. The cases that have been documented show a variation of stakeholders responsible for initiating the process. In some cases it was smallholders approaching other stakeholders for assistance with addressing a challenge, while in other cases it was researchers or extensionists who undertook to develop an innovation to address a challenge that they had encountered through their interaction with smallholders. All documented cases have involved the contribution of ideas, knowledge and skills by at least three different types of stakeholders and the role of local knowledge has been acknowledge through the study. Out of the eleven cases three cases have been selected for a collaborative case assessment which strives to assess further key issues such as actual roles and contributions of various role-players, the dynamics of the innovation process and outcome. Several opportunities arise for joint learning with small scale farmers.