The implementation of Infrared (IR) radiation in heated greenhouses possesses the advantage of high directional control and focused compensation of energy losses, appropriate for creating local microclimate conditions in highly energy-consuming systems, such as greenhouses. Moreover, it can efficiently maintain favorable environmental conditions at the plant canopy. The present study studies the application of Infrared (IR) heating in an experimental greenhouse with eggplant (Solanum melongena L.) cultivation. The experimental results are presented from a full cultivation period inside two identical, small scale experimental greenhouses, with IR and forced air heating system, respectively. The effects of IR heating over plant growth parameters, including the yield of the fruits as well as the total phenolic content and the antioxidant profile of eggplants fruits’ extracts are measured and discussed. The results indicate a greater uniformity production in the IR heating greenhouse in terms of antioxidant and radical scavenging activities, as well as the total phenolic content. Moreover, the phenolic profile of eggplant fruits from both greenhouses revealed the existence of numerous bioactive compounds, some of which were only characteristic of the eggplant fruits from IR heated greenhouses.