Abstract The safety of novel proteins is routinely evaluated in various regulated areas of the food and feed chain, including genetically modified (GM) crops and novel foods (NFs). This project aimed to map the food and feed products containing protein from the main GM crops, relevant food categories falling under the NF Regulation, and unconventional feed, together with their production processes and to discuss the effect of the mapped processes on the safety of the corresponding novel proteins. A scoping literature review (1,325 documents included), an open online survey and a stakeholder workshop were the basis to build up the mappings for products and processes, also including operational conditions for each processing step. In the case of crops, the information gathered also helped identify more than 40 products, and the corresponding production processes, not included in the OECD consensus documents for compositional considerations of GM crops. Moreover, a systematic literature review (154 documents included), carried out within the project, assisted in the identification of the available evidence on the impact of processing on protein safety. Overall, certain processes, such as thermal treatments, fermentation, or enzymatic hydrolysis, significantly enhanced protein digestibility across various food/feed matrices. Similarly, fermentation, ensiling, and extraction processes have been shown to improve nutritional properties in various products. The data collected seemed to indicate that heating can effectively reduce the activity of NEPs from GM crops and that heating and enzymatic hydrolysis can reduce IgE reactivity for certain proteins and operational conditions. However, exceptions to these trends were also reported in the literature, and in certain cases (e.g., impact on gut microbiota), the evidence gathered was insufficient to draw substantiated conclusions. This project also contributed to identify existing knowledge gaps and research needs towards regulatory risk assessment of food and feed products containing protein.