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Abstract Extrusion‐based 3D printing of polymeric biomaterials has emerged as a promising approach for the fabrication of complex tissue engineering constructs. However, the large pore and feature size lead to low cell seeding efficiency and limited control of spatial distribution of cells within the scaffolds. We developed hybrid scaffolds that are composed of 3D‐printed layers and airbrushed fibrous membranes. Airbrushing time was adjusted to fabricate low (L), medium (M), and high (H) density membranes to effectively control stem cell infiltration. When two distinct populations of stem cells were seeded from top or bottom of the scaffolds, scaffolds composed ofLLLmembranes showed gradual mixing of the cells with depth, whereasLHLmembranes led to two distinct regions of cells separated by theHmembrane. Our results demonstrate that fibrous membranes incorporated within 3D‐printed layers enable user‐defined and spatially controlled cell compositions within hybrid scaffolds.