PurposeThis work aims to investigate the current financial structure of Italian agri-food micro, small and medium enterprises (MSMEs) to understand how MSMEs face innovation challenges, which are also required to support sustainable development.Design/methodology/approachTo reach the goal, an empirical longitudinal analysis is performed on a sample of Italian agri-food firms. In detail, to highlight the changes in the use of financial sources between 2013 and 2019, a descriptive ratio analysis is carried out on the data extracted by the AIDA database. In addition, statistical analyses were performed, including t-tests and U Mann–Whitney. Finally, a fixed-effects model is created to analyse the panel data. To ensure homogeneity, the sub-sectors of production and transformation are separately considered.FindingsThe financial structure analysis shows an increase in the equity percentage in the funding sources, attributable to an attempt to compensate for the reduction of banks' funding. However, even though this change has not compromised firms' profitability, the undercapitalisation of companies is still present. Therefore, more equity investments are required to support the innovation process.Originality/valueThe value of the present research is to highlight the choice of using new alternative financing sources instead of traditional banks' credit to implement sustainable and innovative development Italian agri-food sector (AFS). This choice is forced by reducing finance from banks and other financial institutions because of the credit crunch. This issue is even more relevant, considering that MSMEs have structural financial problems but have to fulfil the mission of pursuing innovation in the same way as large companies. Therefore, this paper expands the literature on agri-food, delving into an issue typical of MSMEs and combining agri-food with the need for innovation.