Abstract The adult functional connectome is well characterized by a macroscale spatial gradient of connectivity traversing from unimodal toward higher-order transmodal cortices that recapitulates known principles of hierarchical organization and myelination patterns. Despite an emerging literature assessing connectome properties in neonates, the presence of connectome gradients and particularly their correspondence to microstructure remains largely unknown. We derived connectome gradients using unsupervised techniques applied to functional connectivity data from 40 term-born neonates. A series of cortex-wide analysis examined associations to magnetic resonance imaging-derived morphological parameters (cortical thickness, sulcal depth, curvature), measures of tissue microstructure (intracortical T1w/T2w intensity, superficial white matter diffusion parameters), and subcortico-cortical functional connectivity. Our findings indicate that the primary neonatal connectome gradient runs between sensorimotor and visual anchors and captures specific associations to cortical and superficial white matter microstructure as well as thalamo-cortical connectivity. A second gradient indicated an anterior-to-posterior asymmetry in macroscale connectivity alongside an immature differentiation between unimodal and transmodal areas, indicating a connectome-level circuitry en route to an adult-like organization. Our findings reveal an important coordination of structural and functional interactions in the neonatal connectome across spatial scales. Observed associations were replicable across individual neonates, suggesting consistency and generalizability.