In order to eliminate the possible damage that pesticides can cause to the natural environment and partially protect the ecological balance, scientists and environmentalists continue to work to reduce the environmental burden of pesticides. While natural materials that can be used in the removal of pesticides do not bring an additional burden in terms of environmental pollution, they can contribute to nature's ability to heal itself thanks to their suitable physical structures. In this study, the penconazole molecule, which is widely used as a fungicide in agriculture, was examined theoretically and experimentally. In the theoretical part of the study, the molecular structure of the penconazole molecule was determined by DFT calculations. The calculations were carried out by using B3LYP/ 6-311G(d,p) basis set in the gas phase. Structural parameters, electronic properties, detailed %PED calculation, and vibration wave numbers of the optimized geometry were calculated. MEP map was used to show possible electrophilic and nucleophilic regions. For the experimental part of the study, FTIR, SEM and EDS analyzes of pure hazelnut, walnut, peanut, and cherry seed shells were recorded. Then, fungicide containing penconazole was applied to pure shells, and FTIR, SEM and EDS analyzes were repeated. As a result of this comparison, it was seen that the porous shells adsorbed the pesticide-containing penconazole. The study was supported by comparing theoretical calculations with experimental calculations. FTIR analysis of the fungicide liquid containing the penconazole molecule is in agreement with the theoretically calculated data. After the pure samples were treated with penconazole fungicide, the change in their physical appearance was determined by SEM analysis. EDS analysis revealed this physical change as elemental analysis. Thanks to this study, it has been shown that hazelnut, walnut, peanut, and cherry seed shells are a potentially cheap and environmentally friendly method of removing penconazole from nature.