Comprehensive modification methods for strengthened soils offer a promising approach to mitigating the negative impact of clay minerals and expanding the potential for using clay soils in road pavement construction. Industrial application of comprehensive modification methods for strengthened soils in road construction requires data on the influence of process factors on the physical and mechanical properties of road pavement materials. It has been established that the role of process factors in the comprehensive modification of strengthened soils has not been adequately studied and is a pressing issue when it comes to using complex clay systems in road construction. The study examines the following process factors of comprehensively modified strengthened clay soils that influence changes in the physical and mechanical properties of materials during the construction of pavement layers: the order of component introduction into the soil (water, binder, modifiers), the size of soil aggregates present in the strengthened soil, the compaction coefficient and moisture content, and the duration of the construction process. Graphical and analytical relationships were obtained for the influence of process factors on the compressive strength, flexural tensile strength, and frost resistance coefficient of strengthened soils. It was demonstrated that the use of integrated modification methods enables improved soil strengthened process efficiency. The negative impacts of mixture heterogeneity and insufficient fineness of soil aggregates were reduced, while the efficiency of mechanisms was increased, both during the mixture preparation stage and during subsequent installation of the structural layers of road pavements.