This study, conducted in central Malawi, assessed the way a research intervention using an agricultural innovation system affected rural livelihoods. Propensity score matching was used to establish one village as a control, against which the impact of the intervention on two study villages  could be measured. Using the Enabling Rural Innovation intervention as a case study, it was established that rural livelihood outcomes pertaining to crop and livestock production, household income, asset ownership and fertiliser use were significantly improved by this intervention. In-depth analysis, however, demonstrated that although the participating households had more robust livelihoods during the intervention, when the research programme was phased out the effect was reduced. The authors recommend that local agricultural extension officers should receive more capacity building and budgetary support to ensure proper understanding of agricultural innovation systems concepts and correct application so as to sustain their positive effects.