In developing countries, masonry buildings have become a popular option for housing due to their easy availability of raw materials, thermal and sound insulation benefits, cost-effectiveness, and not requiring skilled labor. However, these structures have limitations such as low tensile strength and ductility and are often built without following standard guidelines. As a result, they have not performed well during seismic events, resulting in significant economic loss and human casualties. Various techniques have been used to mitigate the vulnerability of masonry buildings, but most of these methods focus on external strengthening and, are not economical, require technical expertise, and are time-consuming. These limitations have led to the exploration of internal strengthening techniques. Internal strengthening involves augmenting the mortar properties by reinforcing the mortar. As the performance of the mortar mix plays a crucial role in the overall behavior of masonry structures, improving the mortar properties is imperative. Therefore, this study focuses on improving the seismic behavior of masonry structures by reinforcing waste plastic fiber, coconut fiber, and recycled nylon fiber in the mortar mix. Plastic fibers were obtained from strips of polyethylene terephthalate (PET) bottles, which are commonly used as beverage containers; coconut fibers were extracted from waste coconut shells, and recycled nylon fibers were obtained from waste textile products. Four scale-down two-story masonry structures (one unreinforced and the other three fiber-reinforced) were constructed using a concrete slab and timber roof. Uni-axial shake table test was performed, and parameters such as failure pattern and maximum peak ground acceleration (PGA) were observed. The results showed that the performance of the fiber-reinforced masonry structure was significantly improved compared to the unreinforced one. The fibers in the mortar distributed stress more efficiently, reduced the crack width through fiber-bridging mechanisms, and provided ductility to prevent brittle failure of the structure. The reinforced model sustained a higher maximum PGA value than the unreinforced one. This study highlights the potential of using waste fibers (plastic, coconut, and nylon) to reinforce masonry structures, providing an economical and efficient solution to improve their seismic behavior.