Phosphate fertilizers are critical for crop production in tropical soils, which are known for having high phosphate-fixing capacity and aluminum saturation, as well as low pH and calcium contents. Fluorine is a component of many phosphate rocks used to make phosphate fertilizers, via a process that generates hexafluorosilicic acid (H2SiF6). While many treatment technologies have been proposed for removal of fluorine in industrial facilities, little attention has been given to a process of neutralizing H2SiF6 with calcium oxide aiming to find out an alternative and sustainable use of a by-product with a great potential for beneficial use in tropical agriculture. This study evaluated the effect of a by-product of phosphoric acid production (fluorite with silicon oxide, hereafter called AgroSiCa) on soil properties as well as on growth of soybean and corn. Two experiments (2 crops) were conducted under greenhouse conditions in a completely randomized 3 × 5 × 2 × 3 factorial design as follows: three soils (Red Latosol, Red-Yellow Latosol, and Cambisol), five doses of AgroSiCa (0; 0.5; 1.0; 2.0; 4.0 t ha−1), two doses of phosphorus (2 × %clay and 4 × %clay), with three replicates, totaling 90 plots for each experiment. The application of AgroSiCa resulted in a slight increase of soil pH. Significant increases in calcium, phosphate, and silicon levels in soil solution and in shoots of maize and soybean were observed at all doses of AgroSiCa. We also found very low levels of fluoride in all soil leachates. Significant reduction of labile aluminum was found in all soils after the cultivation of maize and soybean. In sum, AgroSiCa improved soil properties and contributed to a better growth of both crops. Our results show that reacting H2SiF6 derived from the wet-process phosphoric acid production with calcium oxide leads to a by-product with potential for agricultural use, especially when applied in highly-weathered soils. Besides providing calcium and silicon to plants, the use of such by-product in soils with high phosphate-fixing capacity and high aluminum saturation delivers additional benefits, since fluoride and silicon can play an important role in improving soil conditions due to the formation of less plant-toxic forms of aluminum, as well as upon decreasing phosphate fixation, thus improving root development and making fertilizer-derived phosphate more available for plant growth.