Natural fibers and particularly flax fibers have a great potential to replace glass fibers in composite materials. However, the interaction between these fibers and thermoset matrices remains unclear and results in a weak interface affecting the mechanical properties of the composite. This study was carried out to investigate the impact of natural fibers on the chemical reaction between the resin and the hardener, studying the interaction of fibers with each component separately to understand more precisely the phenomena involved. The results show that the contact with the fibers involves a change of the matrix properties that has been attributed to the water absorbed on their surface. On the one hand, water could modify amine functions of the hardener leading to a decrease of 40 degrees C of matrix glass transition temperature (T-g). This issue could be corrected by adding a 16% excess of hardener. On the other hand, the water added to the resin could also accelerate the epoxide/amine reaction increasing slightly the T-g of the matrix and also generating weaker distinct networks of lower T-g by post-modification of the hardener. Therefore, the control of the water content in flax fibers is a crucial parameter for composite manufacturing.