Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip (dfRootChip), a microfluidic organ-on-a-chip platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from root guidance, monitoring of physiology and development under asymmetric conditions, tracing molecular uptake and selective drug treatments to local inoculation with microbes. We measured calcium responses in roots treated with biotic and abiotic elicitors and observed elicitor-specific signal propagation across the root from treated to untreated cells. We provide evidence for non-autonomous positive regulation of hair growth across the root upon exposure to unfavourable conditions on the opposite side. Our approach sheds light on lateral coordination of morphological adaptation and facilitates studies on root physiology, signalling and development in heterogeneous environments at the organ level.