The need to form a system of economic security for the effective operation of financial institutions is determined. Peculiarities of ensuring economic security of different types of financial institutions are found out, characteristic features of functional systems of economic security of financial intermediaries are revealed. It is offered to understand the management of economic security of financial institutions as a direction of management activities aimed at achieving a high level of protection of the institution's resources from the negative impact of internal and external threats by implementing a wide range of management decisions to use available opportunities and resources while providing financial services. The basics of the mechanism of economic security management of financial institutions are formed. It is assumed that the organization of the economic security system of a financial institution is carried out in several stages, such as the formation of the economic security system, ensuring the economic security system, identification, assessment, ranking of threats, and development of countermeasures; assessing the level of readiness of institutions to implement a mechanism for managing economic security; assessment of the level of economic security, development of management decisions. It is determined that the purpose of economic security management is to achieve the maximum possible level of realization of the institution's interests and meet the interests and needs of clients with optimal resource costs to minimize the impact of threats that accompany the activities of institutions.