In Mediterranean basin, citrus culture is expanding rapidly with a growing demand for high-quality saplings. Protected cultivation with fine microclimate conditions control is the best process of citrus saplings growing with the required quality. In this context, the developed microclimate of a tunnel citrus saplings greenhouse and its effects on plant activity parameters, such as leaf temperature and transpiration, were investigated. The findings show that the temperatures of air and plant leaves inside the greenhouse are highly variable between 6 °C and 33 °C and from 8 °C to 30 °C, respectively. Results also show that greenhouse air humidity is very high – more than 80%. The analysis of plant transpiration based on greenhouse microclimate conditions and leaf temperature reveals that (i) plant transpiration varies throughout the day (between 1.9 and 65.7 mg m−2·s−1); (ii) leaf temperature simulation can be used as an indirect indicator of plant water stress; and (iii) the simulated temperature difference between the leaves and the internal air of the greenhouse can be used to define the minimum threshold air temperature for proper plant development under the greenhouse conditions.