Plant health and productivity within the phytobiome are shaped by intricate, simultaneous interactions among diverse organisms and their environment. These complex interactions often produce plant responses that differ markedly from those observed in simplified, single-stressor systems. To build resilient agricultural systems, we must move beyond traditional approaches that examine plant responses to individual stresses in isolation. Instead, it is critical to understand how plants respond to multiple, concurrent challenges—biotic and abiotic—within the context of the full phytobiome. Advancing sustainable crop improvement and management strategies will require a systems-level approach that embraces the complexity of plant-environment-microbe interactions.