Eph‐ephrin signaling acts as spatial cue to define the tissue boundaries, the axonal growth, or the organization of compartmentalized tissues in vertebrates. By the regulation of tension, adhesion, and repulsion, intermingling of cells expressing the membrane‐tethered ligand and cells expressing the membrane‐tethered receptor is prevented. Despite being surface‐bound, most of the studies addressing Eph‐ephrin interactions use soluble ligands, which lack the spatial component needed to study tissue patterning. Here, it is shown that spatial patterns of ephrin ligands can modulate the organization of the different compartments in organoid‐derived intestinal epithelial monolayers. A modified version of the microcontact printing technique is used to create spatial cues of ephrin ligand on basement membrane surrogates. It is shown that both ligand concentration and cellular density can impact the strength of the repulsive effect triggered by Eph‐ephrin signaling. Finally, it is demonstrated that by using micropatterned ephrin spatial cues one can modify the orientation of intestinal crypts and align them in the direction set by the pattern. The approach presented here is believed to be an excellent tool to study exogenous signal with relevant spatial distribution in vivo.