Transformational processes in the global and Russian economy serve as a reason for business entities to search for new ways of producing goods allowing the most efficient use of available resources. Toll processing (in international practice – tolling operations) allows expanding the sphere of business of agricultural formations and, thus, increasing their effectiveness. The complexity of accounting and taxation of operations for toll processing increases the probability of occurrence of tax, accounting, and legal risks, which justifies the necessity to develop a methodology for internal control of these operations. The authors analyzed the results of the financial and economic activities of agricultural formations and made a conclusion about the economic expediency of toll processing operations, both for an organization-conversion material supplier and for a tolling party. The authors carried out the theoretical research and determined the features of accounting for a processor organization, as opposed to a supplier organization. In the process of testing the accounts, typical violations were identified, which are related to the correctness of accounting of tolling business processes, the formation of prime cost, and the taxable base for income tax, which causes tax risks. The authors developed a methodology for internal control of the “Toll processing” business process and the procedure for its reflection in business accounting and fiscal accounting. The following aspects formed the basis of the developed methodological toolkit for internal control of tolling operations: information support; control procedures; a step-by-step approach based on a preliminary risk analysis.