The preservation of soil structural integrity and optimal root development in smallholder agroecosystems is increasingly compromised by conventional, mass-dependent agricultural machinery. This review evaluates the agronomic implications of transitioning from heavy draft power to scale-neutral, autonomous modular swarms within fragmented farming systems (subplots under 2 hectares). Systematic analysis of 40 studies (via Scopus and Web of Science) demonstrates that conventional high-axle-load machinery induces deep subsoil stress cones. These pathways impede essential nutrient uptake, limit water infiltration and ultimately stunt plant physiological development. Conversely, purpose-built, lightweight autonomous platforms confine mechanical load impacts to the topsoil layer. This critical engineering shift preserves subsurface soil porosity, sustains a viable and highly active rhizosphere and prevents long-term structural degradation. Furthermore, the integration of sensor-driven precision navigation facilitates a 15–20 % reduction in basal fertiliser application. This optimises plant nutrient use efficiency while mitigating runoff into surrounding ecosystems. Adopting these systems yields operational efficiencies, including an 8–12 % reduction in overlap and a 6–10 % decrease in fuel consumption. These effects vary by soil texture, moisture and root architecture, being most pronounced in compaction-prone soils (e.g., Vertisols) susceptible to degradation. While socioeconomic barriers to adoption exist for marginal farmers, the primary agronomic benefit of autonomous swarms lies in their immediate capacity to halt anthropogenic soil compaction. Modular autonomous mechanisation offers a promising agroecological pathway, with potential to help maintain subsoil health, promote root proliferation and secure yields in vulnerable environments.