A comparative study of the sensor response toward gaseous ammonia of hexadecafluorinated 3d-metal phthalocyanine (MPcF16, M=Cu(II), Co(II), Zn(II), Ni(II)) thin films was performed using complementary experimental (viz., surface plasmon resonance, SPR, and IR absorption spectroscopy) along with theoretical (density functional theory calculations, DFT) techniques. SPR measurements revealed changes of both thickness and optical parameters (refraction indices and extinction coefficients) of the MPcF16 films caused by adsorption of NH3. The MPcF16 species studied exhibited the following order of sensor response: ZnPcF16 > CoPcF16 ≥ CuPcF16 > NiPcF16. A good correlation was found between the DFT calculated (B3LYP/6-311++G(2df,p)) binding energies, experimentally measured shift of the selected IR bands, and the optical sensor response. Apart from this, we performed a detailed assignment of all intense bands in the vibrational spectra (IR and Raman) of fluorinated 3d-metal phthalocyanines studied.