The present work has developed a methodology based on thermography and sonic anemometry for studying the microclimate in Mediterranean greenhouses equipped with air heaters and polyethylene distribution ducts to distribute the warm air. Sonic anemometry allows us to identify the airflow pattern generated by the heaters and to analyze the temperature distribution inside the greenhouse, while thermography provides accurate crop temperature data. Air distribution by means of perforated polyethylene ducts at ground level, widely used in Mediterranean-type greenhouses, can generate heterogeneous temperature distributions inside the greenhouse when the system is not correctly designed. The system analyzed in this work used a polyethylene duct with a row of hot air outlet holes (all of equal diameter) that expel warm air toward the ground to avoid plant damage. We have observed that this design (the most widely used in Almería’s greenhouses) produces stagnation of hot air in the highest part of the structure, reducing the heating of the crop zone. Using 88 kW heating power (146.7 W∙m−2) the temperature inside the greenhouse is maintained 7.2 to 11.2 °C above the outside temperature. The crop temperature (17.6 to 19.9 °C) was maintained above the minimum recommended value of 10 °C.