Bead-based assays in flow cytometry are multiplexed analytical techniques that allow rapid and simultaneous detection and quantification of a large number of analytes from small volumes of samples. The development of corresponding bead-based assays in mass cytometry (MC) is highly desirable since it could increase the number of analytes detected in a single assay. The microbeads for these assays have to be labeled with metal isotopes for MC detection. One must also be able to functionalize the bead surface with affinity reagents to capture the analytes. Metal-encoded polystyrene microbeads prepared by multi-stage dispersion polymerization can produce effective isotopic signals in MC with relatively small bead-to-bead variations. However, functionalizing this microbead surface with bioaffinity agents remains challenging, possibly due to the interference of the steric-stabilizing PVP corona on the microbead surface. Here, we report a systematic investigation of a silica coating approach to coat Eu-encoded microbeads with thin silica shells, to functionalize the surface with amino groups, and to introduce bioaffinity agents. We examine the effect of silica shell roughness on the bioconjugation capacity and the effect of silica shell thickness on signal quality in MC measurements. To limit non-specific binding, we converted the amino groups on the microbead surface to carboxylic acid groups. Antibodies were effectively attached to microbead by first conjugating NeutrAvidin to the carboxyl-modified bead surface and then attaching biotinylated antibodies to the NeutrAvidin-modified bead surface. The antibody-modified microbeads can specifically capture antigens, which were marked with isotopic labels, and generate strong signals in MC. These are promising results for the development of bead-based assays in MC.