The article explores the correlation between the criminal law qualification of a crime and criminal procedural proof. Based on the analysis of the current version of the Criminal Procedure Code of the Russian Federation, the authors substantiate a two-level structure of proof, within which the establishment of factual circumstances by means of evidence is distinguished from the logical and argumentative justification of legal conclusions. It is shown that qualification is not included in the subject of proof and is not subject to proof as such: what has to be proved is its factual basis, whereas the legal assessment itself is subject to substantiation (reasoning). The article reveals an implicit differentiation between questions of fact and questions of law in Part 1 of Article 299 of the Criminal Procedure Code of the Russian Federation, including the asymmetry of predicates and the legislator’s terminological transition from the category of “act” to the category of “crime”. The programming function of qualification in relation to the subject and limits of proof is disclosed. The authors argue that preliminary qualification does not contradict the presumption of innocence, while noting a deficit of judicial control over the validity of qualification in pre-trial proceedings, which has become particularly significant after the reform of Article 108 of the Code. Proposals for improving criminal procedure legislation are formulated.