The unique spectral, fluorescent, bioactive properties, along with its water solubility, makes R-phycoerythrin (R-PE) a promising natural colorant for food applications. The aim of this study was to investigate stained extrudates with respect to color stability of different purities of R-PE from F. lumbricalis during cold storage in light and dark conditions. Furthermore, the color stability of R-PE during extrusion and in stained meat analogs before and after frying was investigated. The storage stability was evaluated based on the staining with R-PE (crude extract, membrane filtration and multi-step ammonium sulphate precipitation) with beetroot pigment as a reference and at different hydration temperatures (40 and 60 °C). R-PE stained extrudates preserved their structure and color throughout storage without light exposure, unlike beetroot-stained ones, which displayed color changes (ΔE*ab >
5) while keeping their structure intact. Under light exposure, R-PE extrudates shrunk slightly over time, with only subtle color changes (ΔE*ab <
5). The storage stability of R-PE stained extrudates differed based on the R-PE purity, both in light and dark conditions, and also varied with hydration temperature during light exposure. The addition of different purities of R-PE and beetroot pigment during extrusion with expansion resulted in lower color retention in all the resulting extrudates except in the extrudates without expansion. After frying, both unstained and stained R-PE meat analogs developed a darker brown color, but the interior of these analogs preserved their initial color, resembling the color of the meat analogs before frying.