In this paper we investigated the management system of scholarly journals in the university. This topic became valuable in recent years due to the raising interest for the university science as a whole. The paper presents a case study of Peter the Great St. Petersburg Polytechnic University, where the audit of scholarly journals took place. The audit’s goals included: collection of information on all scholar periodicals affiliated to the university; evaluation of its compliance with international publishing standards and internal policies; scientometric analysis. As a result we should formulate the common policy for all scholarly journals published with the university. The paper depicts the main steps of the audit: data collection, subject analysis, compliance with standards and internal documents, scientometric analysis using Scopus and Russian Science Citation Index. As conclusions, we give recommendations that should be used to formulate the common policy of the university in reference to its scholarly journals.