The subject of the study is the problem of organizing internal control in budgetary institutions. The article discusses the theoretical issues of the formation of the system for internal financial control carried out by budgetary organizations of our country. The relevance of assessing the effectiveness of internal financial control in budgetary institutions is determined. The main shortcomings and problematic issues on the organization of internal financial control in the public sector are shown. The need to organize internal control in budgetary institutions does not raise any doubts, not only within the framework of the legislative obligations, but also because of the recognition of the need for effective supervision of the spending of budgetary funds. Control is the main independent source of information for identifying the causes of abuses arising in the process of managing public finances and state property, as well as an effective means of influencing decision-making to prevent certain violations. In such circumstances, the importance of internal control in budgetary institutions is constantly growing. With this in mind, the article reports the study of the features, content, and tools of internal control, as an element of preventing violations in the accounting of a budgetary institution. In the process of analysis, the relationship between the effectiveness of accounting systems and the internal control, which is inversely proportional, is examined. Special attention is also paid to the methods of internal control, self-control, control by the subordination level, control by the jurisdiction level, and the procedure for conducting joint control. The transition to the digital economy, the structural changes resulting from this, and the totality of theoretical, methodological, and practical issues related to the development of organizational and procedural support for internal financial audit entities in the public sector organizations are relevant and most interesting for scientific study. Over the past decade, a radical change in the organization of internal financial audits has taken place, associated with the implementation of international norms and standards in the legislation of the Russian Federation. In accordance with the international concept of state internal financial control, a distinction is made between the functions of internal control and internal audit.