3D cell spheroids have emerged as indispensable tools in cell biology research. In this study, the efficacy of an open-close switchable microfluidic device for on-chip staining and agar-embedding of 3D spheroids was thoroughly validated, especially in preparation for immunohistochemistry (IHC) analysis. The on-chip staining procedure, employing Trypan blue and Calcein-AM/PI staining, was demonstrated to evaluate the cell viability of spheroids. During overextended culture periods, a discernible decline in cell viability was observed at the central region of the spheroids, offering valuable information on the temporal aspects of spheroid development. On-chip agar embedding stands out for its precise control over the location and orientation of three-dimensional spheroids, a key factor in exploring cellular architecture, especially in fused spheroids using IHC analysis. In comparison to tube-based staining, this method significantly cuts down on reagent use and analysis time. This not only boosts efficiency but also lowers the risk of spheroid damage or loss during staining, highlighting its potential for handling miniaturized tissue samples and biopsies in cell assays. The on-chip staining and agar-embedding techniques presented here not only provide valuable insights into spheroids’ behavior but also pave the way for further developments in miniaturized tissue analysis and cell-based assays.