Agroforestry, where trees and shrubs are planted in row-alley systems, can utilize the natural ability of plants to interact with pollutants and serve as a passive biotechnological method for improving air quality. A method for programming air phytoremediation processes is presented, using appropriately shaped plant structures, considering species characteristics and the spatial configuration of plants in row-alley plantings. The main objectives of this study were: to determine the relationship between pollution reduction and the characteristics of plant communities, considering the parameters of individual plants and group characteristics, to determine strategic parameters for the interaction between plants and pollutant flows, and to identify optimization paths for each stage. The optimization of the air phytoremediation process is presented using the example of changes in the fine particulate matter (PM_2.5) concentration pattern, analyzed through numerical experiments using micrometeorological computational fluid dynamics models (ENVI-met software). Ex-ante analysis of hypothetical scenarios showed that introducing appropriate configurations of variable vegetation structure could lead to pollution reductions of up to 19%. The effectiveness of the presented plant systems qualifies this method as a type of bioengineering technology, supporting the multifunctionality of agroforestry systems.