Growth factor (GF) patterning in stem cell spheroids, such as embryoid bodies (EBs), has been sought to guide their differentiation and organization into functional 3D tissue models and organoids. Current approaches relying on exposure of EBs to gradients of GFs suffer from poor molecular transport in the spheroid microenvironment and from high cost of production and low stability of recombinant GFs. We have developed an alternative method for establishing GF gradients in EBs utilizing stem cell surface engineering with membrane-targeting heparan sulfate-glycomimetic co-receptors for GFs. We have capitalized on the ability of amphiphilic lipid-functionalized glycopolymers with affinity for FGF2 to assemble into nanoscale vesicles with tunable dimensions and extracellular matrix penetrance. Upon size-dependent diffusion into EBs, the vesicles fused with the plasma membranes of stem cells, giving rise to concentric gradients of cells with enhanced FGF2-binding. The extracellular matrix-assisted cell surface remodeling process described is the first example of spatially-targeted glycocalyx engineering in multicellular systems to control GF localization. The glycopolymer structure, vesicle dimensions, and remodeling conditions determine the level of FGF2 adhesion and gradient slope. The increased chemical and thermal stability of the synthetic glycomimetics and the tunability of their GF-binding profile, which is defined by their glycosylation and may be extended to other recombinant or endogenous morphogens beyond FGF2, further increase the versatility of this method.