In the face of current global threats, including the COVID-19 Pandemic, new technological solutions are needed. Globalization, progressing urbanization, the decreasing availability of cultivable land for food production, water contamination, flood risk and climate change, can all be viewed as potential threats to food safety. According to forecasts and trends, the future of both agricultural policy and agricultural innovation will be based on big data, data analytics and machine learning. Therefore, it is and will continue to be important to develop information systems dedicated to agricultural innovation and the management of food security challenges. The main aim of the study is a classification of data for a uniform AMIS from data from IREIS, GC and AIIS based on survey and expert interview data obtained. We propose to expand the range of data produced by small farmers while keeping in mind the protection of farmers and their rights and the possible benefits of the data provided. The literature recognizes the value of such data but it has not yet been legally regulated, protected, managed and, above all, properly used for agricultural and food security policy purposes. Therefore, we develop the idea of extended farmers’ participation in the production of agricultural activity data. The research used a survey questionnaire and expert interviews. A viable AIIS needs current data that farmers already produce as well as additional data needs which we identify in our research. We propose an architecture of databases and describe their flow in the Agriculture Management Information System (AMIS).