Multi-cellular aggregates are found in healthy and diseased tissues, and while cell–cell contact is important for regulating many cell functions, cells also interact, to varying degrees, with extra-cellular matrix (ECM) proteins. Islets of Langerhans are one such example of cell aggregates in contact with ECM, both at the periphery of the cluster and dispersed throughout. While several studies have investigated the effect of reintroducing contact with ECM proteins on islet cell survival and function, the majority of these experiments only allow contact with the exterior cells. Thus, cell-culture platforms that enable the study of ECM–cell interactions throughout multi-cellular aggregates are of interest. Here, local presentation of ECM proteins was achieved using hydrogel microwell arrays to incorporate protein-laden microparticles during formation of MIN6 β-cell aggregates. Varying the microparticle seeding density reproducibly controlled the number of microparticles incorporated within three-dimensional aggregates (i.e., total amount of protein). Further, a relatively uniform spatial distribution of laminin- and fibronectin-coated microparticles was achieved throughout the x-, y-, and z-directions. Multiple ECM proteins were presented to β-cells in concert by incorporating two distinct populations of microparticles throughout the aggregates. Finally, scaling the microwell device dimensions allowed for the formation of two different sized cell–particle aggregates, ∼80 and 160 µm in diameter. While the total number of microparticles incorporated per aggregate varied with size, the fraction of the aggregate occupied by microparticles was affected only by the microparticle seeding density, indicating that uniform local concentrations of proteins can be preserved while changing the overall aggregate dimensions. Biotechnol. Biotechnol. Bioeng. 2014;111: 1028–1037. © 2013 Wiley Periodicals, Inc.