The paper describes a protocol to fabricate cell-laden microgel assemblies with pre-defined micro-architecture and complexity by a bottom-up approach, which can be used for tissue engineering applications. The assembly process was driven by the hydrophobic effect in the water/oil interface. By agitating hydrophilic microgels in hydrophobic medium, the shape-controlled microgel units assemble in an organized manner to locally minimize the interaction free energy (the surface area exposed to the oil). The assembly process was shown to be controlled by several parameters, such as external energy input, surface tension, and microgel dimensions. This assembly approach was used to build multi-component cell-laden constructs by assembling microgel building blocks and performing a secondary cross-linking reaction. This bottom-up approach for the directed assembly of cell-laden microgels offers a scalable method to fabricate 3D tissue constructs with biomimetic structure.