The multi-level perspective (MLP) is a prominent transition framework. The MLP posits that transitions come about through interaction processes within and among three analytical levels: niches, socio-technical regimes and a socio-technical landscape. This systematic review provides an overview on the use of the MLP in research on agro-food sustainability transitions. In particular, it analyses the understanding, conceptualisation and operationalisation of niches, regimes and landscapes. Niches considered in the selected papers include agro-ecology, organic agriculture, permaculture, conservation agriculture, integrated farming, and alternative food networks. Regime refers to industrial, conventional agriculture. The researched regime is often not clearly described and its operationalisation is a matter of deliberation. Landscape level is generally overlooked; when it is considered it refers to international trends and developments. Many scholars highlight the inadequacy of transition pathways in the MLP for the agro-food sector. Moreover, transition impacts are rarely addressed and the research field generally overlooks the analysis of the sustainability of niches and, consequently, of transitions. Research on transitions in the agro-food sector borrows from the MLP its generalizability and poor empirical operationalisation of niche, regime and landscape concepts. Therefore, integrative conceptualisation and operationalisation of the MLP elements is required to accommodate the complexity of sustainability transition processes and the peculiarities of the agro-food system.