Microglia are multifunctional immune cells within the brain. In the circadian pineal gland (PG), these phagocytes interact with other cell populations and constituent elements to finely modulate their development and function. As long-lived cells, microglia participate in changes that occur during normal aging, such as alterations in the architecture and functionality of subcellular organelles. Herein, we studied the expression pattern of the lysosomal and associated compartments marker ED1/CD68 in the PG from old male Wistar rats by using multiple immunofluorescence staining followed by quantitative confocal microscopy. Our results showed that the pineal Iba1+ cell population is composed of different subtypes according to the arrangement and cytoplasmic distribution of ED1, in both 3- and 18-month-old samples. However, our quantitative analysis revealed significant changes in the relative density of each phenotype with respect to age. To evaluate the functionality of the different ED1+ structures, we studied the expression of the lysosomal protease cathepsin D. Immunoreactivity for this enzyme in the aged PG suggests that microglia with ED1+ bodies might retain certain proteolytic capacity. Our results indicate that the pineal microglia themselves undergo many changes across their lifespan, including their phagocytic capacity. Microglia, as a plastic and resilient cell population, may continue to influence PG homeostasis and function even as the PG ages.