Living tissues consist of many individual cells, each with their specialized functions, assembled into a higher-order structure. Advances in artificial cells, engineered materials that mimic functions of biological cells, suggest that artificial tissues or hybrid tissues comprising both artificial and living cells could one day be used for drug delivery, biosensing, tissue regeneration, or fundamental biology. The assembly of such prototissues requires programmable and site-specific adhesion between artificial cells that make up the tissue. Toward this goal of creating programmable, spatially organized prototissues, we developed a modular, bioorthogonal conjugation method for attaching proteins to lipid vesicles using covalently inhibited enzymes. We then designed synthetic adhesion proteins that enable vesicle-to-vesicle adhesion between not only specific populations of vesicles but also specific regions of the vesicle surface. Finally, we demonstrate that our synthetic adhesion toolkit allows for controlled binding between artificial cells and natural cells to form hybrid cell aggregates. Together, this work expands the toolbox for controlling synthetic lipid-based particle adhesion to enable hierarchical, spatially controlled structures for applications in chemistry, biology, and materials science.