In today's complex digital business world, almost every company understands the importance of introducing innovations in the process of operation. At the same time, the issues of diagnosing and assessing the results of the chosen innovative path using a marketing audit remain relevant for the reason that there is simply no ready-made template or algorithm for conducting a marketing audit of a company. The problem is the ambiguous definition of a set of indicators for the marketing audit procedure. The purpose of the work was to determine the importance of conducting a marketing audit in the process of managing an innovative company using the algorithm and metrics of a marketing audit. The methodological basis of the study was a review of scientific works of Russian and foreign authors on the issues of conducting marketing audits and an analysis of the operating features of companies involved in the development and implementation of innovations. The specific features of managing an innovative company were identified, and the methodological and methodological problems of conducting a marketing audit of an innovative company were identified. The results of the study showed that the approaches existing in foreign and domestic literature that describe the process and mechanics of conducting a marketing audit are fragmentary. The work proposed its own algorithm for conducting a marketing audit, and identified a set of additional quantitative indicators (metrics) for a more complete and comprehensive procedure for conducting a marketing audit for managing the innovative activities of a company operating in conditions of uncertainty, risks and competition. The article substantiated the importance and relevance of introducing a marketing audit algorithm. The results of the study can be used by innovative companies when conducting a marketing audit procedure.