In this study, the characterization of phosphate rock and natural zeolite, both from Mexico, was carried out and were applied as natural fertilizer. Through X-ray fluorescence (XRF), the chemical composition of the rocks was determined. The minerals detected using X-ray diffraction (XRD) in the natural zeolite and phosphoric rock were mainly clinoptilolite-heulandite and fluorapatite, respectively, and their presence was confirmed by Infrared spectroscopy studies (FTIR). Through scanning electron microscopy (SEM), a significant amount of euhedral crystals of tabular and orthorhombic habit were observed in the natural zeolite and hexagonal crystals in the phosphate rock. Phosphate rock, zeolite, and zeolite exchanged with ammonium ions were used to evaluate their potential application in the pre-harvest stage of Solanum lycopersicum Pai Pai® variety. The plants were grown in the soil inside a greenhouse with zenith ventilation. Afterward, phenological development was studied for 12 weeks. The results were compared with those obtained in a conventional nutritional fertigation system. In conclusion, the proposed system allows a healthy growth similar to that obtained in the conventional fertigation system, confirming viability for its use in the pre-harvest stage of Solanum lycopersicum.