Despite its potential to increase the sustainability of agricultural systems, intercropping has virtually disappeared from the agricultural landscapes of European countries. What impedes its use? The present report focuses on the identification of the barriers to the use of intercropping at each level of the food value chain within the Co-Innovation Case Studies (CICS) involved in the project IntercropVALUES. In total, 189 barriers to the use of intercropping were identified, among which 44% are CICS-specific, therefore proving the relevance of developing context-specific solutions to promote the use of this practice. These barriers were organised in two classifications. Our work shows (i) that all levels of the food value chain are impacted by some barriers, and (ii) that there is a diversity of barrier types preventing the use of intercropping. Nevertheless, both classifications resulted in an unbalanced distribution of barriers between categories. The classification by level of the food value chain revealed that over 50% of the identified barriers affect farmers’ level. Although the percentage of barriers affecting farmers may be overestimated due to a bias from both CICS leaders and us, it probably also reflects an important truth: farmers face more barriers than the other levels of the food value chain when trying to use intercropping, as well as more external barriers, i.e., barriers imposed by other stakeholders, than the other levels of the food value chain. The classification of barriers by type underlined the importance of knowledge-related barriers. This observation raises two questions: i) “were the previous scientific studies regarding intercropping adequately designed to answer to the specific issues faced by stakeholders of the food value chain?”, and ii) “Is the knowledge transfer from researchers to stakeholders of the food value chain sufficient and efficient?”. Finally, the cross-analysis of the two barrier classifications showed that the barrier types affect the different levels of the food value chain differently.