This work is aimed at the development of new heterostructures based on cobalt phthalocyanines (CoPc) and gold nanoparticles (AuNPs), and the evaluation of the prospects of their use to determine low concentrations of ammonia and nitric oxide. For this purpose, CoPc films were decorated with AuNPs by gas-phase methods (MOCVD and PVD) and drop-casting (DC), and their chemiresistive sensor response to low concentrations of NO (10–50 ppb) and NH3 (1–10 ppm) was investigated. A comparative analysis of the characteristics of heterostructures depending on the preparation methods was carried out. The composition, structure, and morphology of the resulting hybrid films were studied by X-ray photoelectron spectroscopy (XPS) and inductively coupled plasma atomic emission (ICP-AES) spectroscopy, as well as electron microscopy methods to discuss the effect of these parameters on the sensor response of hybrid films to ammonia and nitric oxide. It was shown that regardless of the fabrication method, the response of Au/CoPc heterostructures to NH3 and NO gases increased with an increase in the concentration of gold. The sensor response of Au/CoPc heterostructures to NH3 increased 2–3.3 times compared to CoPc film, whereas in the case of NO it increased up to 16 times. The detection limits of the Au/CoPc heterostructure with a gold content of ca. 2.1 µg/cm2 for NH3 and NO were 0.1 ppm and 4 ppb, respectively. It was shown that Au/CoPc heterostructures can be used for the detection of NH3 in a gas mixture simulating exhaled air (N2—74%, O2—16%, H2O—6%, CO2—4%).