Agroecological practices rely on organic inputs to achieve sustainable food systems, often resulting in changes in soil environments. Yet, we have limited understanding on how soil changes impact crop physiology, including crop nutrient acquisition strategies, especially throughout the entire course of an agroecological transition. In this study, we applied a functional trait ecology lens to understand the effects of agroecological practices on crop physiology at various phases of transitioning from conventional agriculture to agroecological systems. To achieve this, we studied 44 maize growing farms in three regions of central India to measure crop leaf and root trait expression shifts over five identified phases of transitioning to natural farming systems. Our results reveal significantly higher variability in maize root traits compared to leaf traits, with specific root length, specific root area, and specific root length density exhibiting the widest variation. Root traits exhibited strong sensitivity to the phase of agroecological transition and farm region. In contrast, most leaf traits, including specific leaf area, leaf nitrogen concentration, and leaf C:N ratios, were more conserved. Principal component analysis showed a clear pattern in root functional traits, and crop trait hypervolume space changed detectably along the transition gradient. Our findings suggest that root traits are more responsive than leaf traits as indicators of agroecological change, which can inform the monitoring of agroecological transitions. By providing quantitative evidence of trait change, this study contributes a novel understanding of the temporal dynamics of crop strategies when farms transition towards sustainable agricultural systems.