Producing enough healthy food for a globally growing urban population within planetary boundaries requires more resource-efficient and localized food production systems. Controlled-environmental food production systems (CEFPS) are a widely discussed new approach for sustainable food production in urban contexts. However, little research has addressed innovation processes of CEFPS in urban or rural areas. This paper aims to address this research gap by adapting an innovation system perspective, developing a conceptual framework for ‘urban food production innovation systems’ (UFoPrInS) and applying it to a paradigmatic case study in Berlin. Based on a content analysis of the relevant literature and 23 semi-structured expert interviews, we analyse (a) the main characteristics and (b) the key elements of the UFoPrInS and their relationships during different stages of the innovation process. The case results show that UFoPrInS faces various challenges related to possible structural failures that can occur in infrastructure, interactions, capabilities of actors and institutions. The current institutional framework at EU and national level was seen as the major barrier to innovations. To support new food production innovations, a comprehensive regulatory framework for CEFPS is needed that considers in an integrated approach the specifics of (1) the highly-intensive production processes, (2) the diverse types of products and (3) the urban location.