This work studied the chemical composition, cure characteristics, and morphological and mechanical properties of natural rubber (NR) compounds filled with silica, which was derived from bagasse ash (BA). The BA filler underwent various preparation processes (untreated, hydrochloric acid (HCl)-treated, and HCl/ammonium fluoride (HCl/NH4F) extracted). The results revealed that the main functional group of the BA was silica. After purification by HCl and HCl/NH4F, the silica content increased from 77.2% to 90.6% and 97.0%, respectively. Longer cure times and lower crosslinking were obtained after purifying the silica. Treatment of silica with HCl/NH4F improved the tensile strength and compression set when added at 15 parts per hundred rubber (phr) loading. Purification with HCl and HCl/NH4F acted as an obstacle to rubber-rubber crosslinking, but helped to moderate the filler–filler interaction. The elongation range for the NR containing the BA silica in this work was 900% to 1,100%. The use of HCl/NH4F-extracted silica in NR vulcanizates had no effect on the lightness, while the untreated and HCl-treated silica displayed decreased lightness. The silica from BA is recommended for use as reinforcing filler in NR compounds if treated with HCl followed by NH4F extraction before use. The optimal loading of the treated silica was 15 phr.