The formation of drug carriers able to incorporate multiple molecular payloads in separate compartments was investigated, using the hetero-aggregation of oppositely charged hydrogel microparticles as the building blocks. The primary particles – negatively charged alginate and positively charged chitosan microgels with a mean diameter of 6–7 μm – were produced by spray drying with in situ cross-linking. The kinetics of their hetero-aggregation was measured on-line by static light scattering. The effects of the starting stoichiometry (positive:negative particle ratio), hydrodynamic conditions (agitation intensity), and pre-conditioning (dry vs. pre-hydrated primary particles) on the aggregate growth rate were systematically investigated. An optimum stoichiometric ratio of the primary particles was found in each case. The structure of the resulting hetero-aggregates was characterised by laser scanning confocal microscopy and found to strongly depend on the pre-conditioning of the primary particles. While dry primary particles resulted in open, floccular structures, pre-hydrated primary particles gave rise to relatively dense, compact aggregates. The ability to incorporate multiple molecular payloads was demonstrated, providing a platform for the formation of well-defined structures that can be further used in applications such as the encapsulation and release of multiple actives from a single carrier.