A key factor for achieving healthy environments in residential buildings is the provision of high indoor environmental quality (IEQ) with respect to the acceptance by its occupants, based on levels of the physical parameters which contribute to IEQ. This research focuses on defining the comfort standards of indoor environments of urban dwellings in the city of Cuenca—Ecuador. It takes into account factors such as temperature, air quality, and natural lightning through a mixed method of quantitative and qualitative measurements. Results determined the following values: a comfort temperature (Tn) of 20.12 °C (with ranges from 16.62 °C to 23.62 °C for an acceptance of 80% and from 17.62 °C to 22.62 °C for an acceptance of 90%), a relative humidity between 40–65%, a maximum CO2 concentration of 614.25 ppm, a day light factor of ≥5 for the social area and ≥4 for the bedroom, and a minimum illumination level of 300 lux. With these results, it was observed that the comfort levels of temperature, CO2 concentration, and lighting accepted by local users differ from the standards established in local and international regulations. The determined data constitutes a methodological basis for carrying out similar processes in other localities.