The delivery of lipophilic dyes, such as BODIPY 505/515, to cells is often hindered by their low aqueous solubility, necessitating the use of organic solvents to facilitate the delivery, which unfortunately compromises the viability of the cells. In this work, we demonstrate the generation of novel composite hydrogel microparticles loaded with BODIPY 505/515, which can be used to deliver the dye to microalgal cells to stain the intracellular lipids. The microparticles were prepared by combining polymeric micelles with hydrogel technology to obtain microparticles of enhanced loading capacity. The generated hydrogel microparticles were tested by incubation with Phaeodactylum tricornutum algal cells. The cells were rapidly and successfully stained by the dye-containing microparticles, and their viability was not affected by the staining process. The method can also be used to stain other types of microalgal cells, such as Nannochloropsis gaditana cells. We therefore believe that this work offers a versatile and useful solution to important cell-staining problems in biotechnology.