Nanoplastics are widely distributed in crop soils and can interact with other exposed organic contaminants such as pesticides, leading to enhanced toxicity to plants and soil-beneficial microorganisms. These combined organic pollutants can also interact physiochemically with mineral matrices, becoming selectively preserved and occluded. Inclusion organics within growing minerals and the pore spaces of mineral aggregates are potentially inaccessible to plant root cells and soil microorganisms due to the limitation of their movement, but the microscopic mechanisms that control occlusion processes in the presence of nanoplastics mixed with pesticides remain poorly understood. Here, we use time-resolved atomic force microscopy (AFM) to observe how model soil minerals interact in situ with different functional groups of polystyrene (PSFG) mixed with glyphosate (PMG). Our results show that the PSFG–PMG complexes are occluded within calcite and iron hydroxide particles through hillock growth and aggregation, respectively. The free energies of binding between the functional groups of polystyrene and calcite surfaces measured using AFM-based dynamic force spectroscopy in the presence of different concentrations of PMG account for the molecular interactions involved in the occlusion process and the effects of the PMG concentration. These in situ nanoscale observations and molecular-scale energetic measurements in a simple model system may provide insights into the immobilization of both nanoplastics and pesticides by soil minerals, with potential implications relating to multiple pollutant sequestration.