The article states that to achieve the advanced development in agrarian sector and to ensure food sovereignty of Russia it is required to introduce a digital economy model. Diffusion of financial digital innovations into agriculture can occur through industrial adaptation of platforms and technologies, on the basis of which general and specific competencies are formed to develop payment and adjacent markets. The identified tendencies indicate towards the reduction in physical presence of banks and other financial institutions located in the peripheral territories relating to the federal center that could be agents of digital innovations in agribusiness sector. The applicability of new technologies (cloud technologies, big data, artificial intelligence and robotics, open interfaces (API), biometrics, distributed registries, mobile contactless technologies) used by representatives of agribusiness is considered. It is proposed to develop the regional banking sector and the regional payment infrastructure that create conditions not only for leveling the economic development of the regions, but also making it possible to increase the availability to innovative financial technologies that can be used in agribusiness and in other traditional industries. We propose the measures of territorial diversification to make payments and of the infrastructure development and of the diffusion of digital payment innovations used in agriculture.