The present study investigates the preference index of natural fibers such as sisal, coir, and rice straw fibers in stone matrix asphalt mixtures (SMA), using waste marble as filler. Waste marble was used as the filler in asphalt mixtures and was crushed by abrasion machine and sieved according to SMA filler requirements. The SEM topography and EDS analysis of sisal, coir, and rice straw fibers were also carried out. The Marshall test was conducted, which is the most acceptable, cost-effective, and widely adopted method to estimate the optimum bitumen and to examine several Marshall Measures, such as flow value, voids filled with bitumen (VFB), stability, voids in mineral aggregate (VMA), and air voids (VA). Furthermore, tests were performed on the specimen with the optimum amount of bitumen, different percentages of fibers, and waste marble as filler to calculate drain down, moister sensitivity, and Marshall Stability. Multi-criteria decision-making (MCDM) techniques were implemented to obtain subjective and objective weights, which were further used to compute the values of the preference index of natural fiber contents. The outcomes revealed favorable results for the usage of marble dust as filler in Stone Matrix Asphalt (SMA). In addition, the preference index upshots are inclined toward the usage of rice straw over coir followed by sisal fiber. It was observed that the value of the preference index in rice straw at 0.3 varied from 0.918, 0.925, and 0.931 in rice straw using equal, objective, and subjective weights, respectively. The maximum drain down value observed is 0.335 based on ASTM-D 6390 and IRC-SP-79 are against 0.3 percent natural fiber. Moreover, as per the prescribed limit of MoRTH, because of the thin film around aggregates, moisture susceptibility characteristics, i.e., better resistance to moisture, were enhanced by more than 80%.