A significant proportion of entrepreneurs as well as Russian population in general consider the possibility of criminal prosecution to be one of the main problems that hinders business development in Russia. However, only a small proportion of entrepreneurs are subjected to this type of prosecution. The current study attempts to empirically test the hypothesis about the negative impact of unjustified criminal prosecution on entrepreneurial activity. First, we examine the mechanism of unjustified criminal prosecution of entrepreneurs and then using mixed effects regression modelling on panel data for 2017—2021 assess its impact on the growth rate of the number of small and medium-sized enterprises (SMEs). The number of appeals reviewed by the Center for Public Procedures “Business against corruption” (CPP “BAC”) is used as an indicator of unjustified criminal prosecution. The results show that each additionally handled appeal reduces the rate of growth in the number of SMEs in the medium term. This relationship is explained via the theory of signals: appeals to the CPP “BAC” serve as indicators of unjustified prosecution problem for entrepreneurs. If this problem persists, a decrease in the growth rates of firms, and an increase in their number in the shadow economy can also be expected.