In this work, the sensor response of MPcFx (M = Cu, Co, Zn; x = 0, 4, 16) films toward gaseous NH3 (10-50 ppm) was studied by a chemiresistive method and compared to that of unsubstituted MPc films to reveal the effects of central metals and F-substituents on the sensing properties. A combination of atomic force microscopy and X-ray diffraction techniques have been used to elucidate the structural features of thin MPcFx films deposited by organic molecular beam deposition. It has been shown that the sensor response of MPcF4 films to ammonia is noticeably higher than that of MPc films, which is in good correlation with the values of binding energy between the metal phthalocyanine and NH3 molecules, as calculated by the density functional theory (DFT) method. At the same time, in contrast to the DFT calculations, MPcF16 demonstrated the lesser sensor response compared with MPcF4, which appeared to be connected with the different structure and morphology of their films. The ZnPcF4 films were shown to exhibit a sensitivity to ammonia up to concentrations as low as 0.1 ppm, and can be used for the selective detection of ammonia in the presence of some reducing gases and volatile organic compounds. Moreover, the ZnPcF4 films can be used for the detection of NH3 in the gas mixture simulating exhaled air (N2 76%, O2 16%, H2O 5%, and CO2 3%).