Innovations supporting a shift towards more sustainable food systems can be developed within the dominant food system regime or in alternative niches. No study has compared the challenges faced in each context. This paper, based on an analysis of 25 cases of European innovations that support crop diversification, explores the extent to which barriers to crop diversification can be related to the proximity of innovation settings with dominant food systems. Drawing on a qualitative analysis of interviews and participatory brainstorming, we highlight 46 different barriers to crop diversification across the cases, at different levels: production; downstream operations from farm to retailing, marketing and consumers; and contracts and coordination between actors. To characterise the diversity of innovation strategies at food system level, we introduce the concept of "food system innovation settings" combining: (i) the type of innovative practice promoted at farm level; (ii) the type of value chain supporting that innovation; and (iii) the type of agriculture involved (organic or conventional). Through a multiple correspondence analysis, we show different patterns of barriers to crop diversification according to three ideal-types of food system innovation settings: (i) "Changing from within", where longer rotations are fostered on conventional farms involved in commodity supply chains; (ii) "Building outside", where crop diversification integrates intercropping on organic farms involved in local supply chains; and (iii) "Playing horizontal", where actors promote alternative crop diversification strategies-either strictly speaking horizontal at spatial level (e.g. strip cropping) or socially horizontal (arrangement between farmers)-without directly challenging the vertical organisation of dominant value chains. We recommend designing targeted research and policy actions according to the food systems they seek to develop. We then discuss further development of our approach to analyse barriers faced in intermediate and hybrid food system configurations.