The Multidisciplinary Digital Publishing Institute (MDPI) is a prominent open access (OA) publisher that uses article processing charges (APCs) as its business model. Our objective was to determine the association between the APCs levied by MDPI journals and 1) their inclusion in Scopus and Web of Science databases or 2) their stature, as represented by their CiteScore (Elsevier’s Scopus) and Impact Factor (awarded by Clarivate Analytics). Among the 227 journals published by MDPI, 51 had both IF and CiteScore; 107, only a CiteScore; and 84, neither IF nor CiteScore. The charges levied by the journals varied widely, from 0 to CHF 2000 (Swiss francs), the most frequent figure (159 journals) being CHF 1000, or about €930. The amount of APCs was found to be correlated to IF (R² = 0.64; p <0.001; 107 journals) and also to CiteScore (R² = 0.619; p <0.001; 53 journals). The charges levied by journals that had both IF and CiteScore were significantly higher than those charged by journals with neither IF nor CiteScore (p <0.05). The charges were also correlated to the age of the journal: the more recently launched journals charged less than the older journals did.