It is necessary to use adsorbents derived from natural materials, such as biosorbents since they do not any damage to the environment, for pollutants elimination that contaminate the aquatic environment. Since the deficiency in the literature was determined in the study in which only the adsorbent obtained from tomato stem was used before this study, a waste material with tomato stem was selected as a natural adsorbent without chemical compounds. Phosphate and dye contaminants, which are often present in industrial and municipal wastewater, were eliminated by adsorption process. Fourier transform infrared (FTIR), x‐ray fluorescence (XRF), Zeta potential, and scanning electron microscope (SEM) with energy dispersive x‐ray (EDX) spectroscopy were used to analyze tomato stems. The tomato stems resulted in high pollutants removal efficiencies recording 99.31% of phosphate () removal efficiency and 99.44% of Direct Orange 46 (DO 46) dye removal efficiency at optimal conditions. The best conditions for phosphate adsorption were pH = 6.0, 2.0 g/L of tomato stems concentration, 50 mg/L initial phosphate concentration and a contact time of 120 min resulting in an adsorption capacity of 4.24 mg/g. The best conditions for DO 46 adsorption were pH = 12, 2.0 g/L of adsorbent concentration, initial dye of 200 mg/L concentration and a contact time of 120 min (q = 13.76 mg/g). For both adsorption experiments, the adsorbent size was chosen to be less than 500 μm. As a result of the adsorption experiments on tomato stem ash, Freundlich isotherm (R2: 0.94) was suitable for DO 46 dye adsorption and Temkin isotherm (R2: 0.99) was suitable for elimination. The phosphate (R2: 0.97) and dye (R2: 1) adsorption onto tomato stem ash was explained using a pseudo‐second‐order kinetic model. It has been determined that the adsorption of the DO 46 dye with the tomato stem ash is an exothermic (∆H: −3.174) process that occurs naturally due to its nature (∆G: −8.41). On the other hand, it was determined that the adsorption of was spontaneous (∆G: −5.21) and endothermic (∆H: 5.7357). According to the adsorption results obtained in this study, it is appropriate to use the tomato stem, which is generated as waste, as an adsorbent. It is thought that obtaining from bio‐based waste in the removal of pollutants such as dye and phosphate in water will both reduce the cost and create an advantage in terms of biodegradability.