A procedure is presented for in situ determination of the frequency penetration depth of coated mirrors in Fabry-Perot (FP) based refractometers and its influence on the assessment of refractivity and pressure. It is based on assessments of the absolute frequency of the laser and the free spectral range of the cavity. The procedure is demonstrated on an Invar-based FP cavity system with high-reflection mirrors working at 1.55 μm. The influence was assessed with such a low uncertainty that it does not significantly contribute to the uncertainties (k = 2) in the assessment of refractivity (<8 × 10-13) or pressure of nitrogen (<0.3 mPa).