Type 2 diabetes mellitus (T2DM) represents a major global public health challenge, and bioactive compounds have been investigated as complementary nutritional strategies for disease management. This study evaluated, for the first time, the effects of carotenoids and chlorophylls (lipophilic extract) of Scenedesmus obliquus on the cecal pigment profile, short-chain fatty acids (SCFAs), metabolic parameters, and intestinal fate in an experimental model of T2DM. Healthy and diabetic Wistar rats were supplemented for 28 days with the lipophilic extract (300 mg/kg body weight), alone or in combination with metformin (150 mg/kg bw). Chlorophyll a and all-trans-lutein were the predominant in the extract, whereas all-trans-lutein and chlorophyll derivatives predominated in the cecal contents. β-Carotene-5,6,5′,8′-diepoxide and porphyrins were detected exclusively in the cecum, indicating extensive metabolic transformations during gastrointestinal digestion. Supplementation significantly reduced blood glucose levels and favorably modulated the SCFA profile, restoring the acetate-to-propionate ratio to values comparable to those of healthy animals. Although total cecal pigment content did not differ among groups, carotenoids and chlorophyll derivatives exhibited distinct accumulation patterns, suggesting differential intestinal metabolism. Overall, the findings indicate that the host metabolic status modulates the intestinal fate of microalgal pigments, supporting their potential contribution to glycemic regulation and intestinal fermentation in T2DM.