Whole-canopy gas exchange provides a more accurate measurement of CO2 assimilation (Ac) and transpiration (Ec) compared to single-leaf. The objectives of this study were to evaluate whole-canopy gas exchange of 2 coffee species: Coffea arabica cv. Catuaí Amarelo-Catuaí and Coffea canephora cv. Emcapa 8111 Clone 02–Clone 02 during two different seasons varying in temperature. Six plants >1-year-old of each species were grown in pots (100L) in a greenhouse. Soil moisture was maintained at field capacity. Data were continuously collected for 10days during spring (September 2014—moderate temperatures) and summer (February 2015 with high temperature) and micrometeorological variables were monitored inside the greenhouse. Catuaí had a lower area leaf and higher branch angle resulting in greater light distribution within the canopy that contributed to higher net photosynthesis and transpiration as compared to Clone 02 in both seasons. Catuaí had reduced whole-canopy CO2 assimilation and transpiration during summer, mainly linked to reduced whole-canopy conductance. However, Clone 02 had similar whole-canopy CO2 assimilation and transpiration values in both seasons. Despite reduced gas exchange for Catuaí during summer, the relationship between Ac and Ec indicated that Catuaí had a greater instantaneous WUEc than Clone 02 during spring and there were no differences between species during summer. The dense canopy architecture of Clone 02 limited whole-canopy gas exchange due to poor light distribution within the canopy whereas Catuaí had better canopy light distribution resulting in higher photosynthetic rates than Clone 02 during spring. Additionally, the architecture had a negative effect when Catuaí experiences increased temperature that reduced whole-canopy conductance. High temperatures may limit the growth and production of coffee plants in tropical areas.