Recently, there has been renewed interest in the incorporation of plant fibers in cementitious materials to substitute synthetic, steel, and polymer fibers. This interest has been mainly stimulated by the numerous inherent advantages in the use of natural fibers in composites, such as high supply and availability, cost-effectiveness, low density, and full recyclability. Despite the great interest in incorporating plant fibers in cement, the low compatibility between the fibers and cement generates several problems in the fresh and hardened states of the composite. This work aimed to enhance the mechanical behavior of a cement mortar by incorporating short flax fibers treated with a citric acid solution. This eco-friendly treatment was used to modify the flax fibers in order to improve their physicochemical compatibility with the cement matrix. The fibers were treated with a 5 wt.% citric acid solution, and the effects of the treatment were evaluated by analyzing the properties of the fibers’ surfaces and resulting composite. The mechanical behavior of the fiber-reinforced composite was evaluated on the samples prepared from treated and untreated fibers and compared with that of a control mortar through three-point bending and compression tests and the determination of the toughness index. The treatment was shown to be effective in modifying the surface roughness and wettability of the fibers and resulted in a 41% decrease in their water saturation rate. The cement mixture with treated fibers showed a considerable decrease in the initial setting time delay (24%), and the flexural strength was improved by 43.5% at 7 days and 18% at 28 days compared to that of the control mortar. Despite the expected decrease in the compressive strength of the composites compared to that of the control mortar, the composites containing the treated fibers showed a better performance (13% at 7 days and 6% at 28 days) than those prepared with the raw fibers. It can be concluded that treatment of flax fibers with 5 wt.% citric acid solution shows promise as a way of improving the mechanical properties of the cement mortar and could be beneficial for the production of higher quality composite materials.