The data set presents the presence or absence of barriers to crop diversification at different levels of value chain across contrasted European case-studies. Data were collected based on participatory workshops involving a causal analysis of challenges of crop diversification and complementary interviews with the 25 innovations teams of case-studies at the chore of the DiverIMPACTS project (https://www.diverimpacts.net/). These data account for the initial perception of barriers in the initial phase of the innovation project and may have evolved since. For more information about the data collection and project and further discussion, please refer to the paper "Innovating within or outside dominant food systems? Different challenges for contrasting crop diversification strategies in Europe" of Morel et al. submitted to the journal Plos One.