The main human sources of carotenoids are fruits and vegetables. Some bacteria also synthesise carotenoids that can have peculiar chemical structures that raise the question of their bioavailability in humans. Bacillus indicus HU36 and Bacillus firmus GB1 strains contain glycosyl carotenoids that are partially acylated by linear fatty acids. The aim of the present study was to assess the bioaccessibility, the uptake efficiency and the tissue distribution of these bacterial carotenoids. β-carotene was used as a model carotenoid for comparisons. Results of in vitro digestion experiments showed that bioaccessibility of purified extracts of bacterial carotenoids was considerably higher (about 4.5 times as high) than that of pure β-carotene. Bacterial carotenoids were also bioaccessible when digested from their natural matrices, but about 2 times less than their purified extracts. Bacterial carotenoids were absorbed by Caco-2 with similar efficiency as β-carotene, i.e. about 10%. Bacterial carotenoids were recovered in significant amounts in their native chemical forms in plasma, liver and in adipose tissue of rats, which were force-fed for 3 days with either bacterial carotenoid extracts or lyophilised bacteria. Bacterial carotenoids were found at higher concentrations in rat tissues than β-carotene, about 2–3 times for GB1 carotenoids and 9 times for HU36 carotenoids. They were also more recovered in adipose tissue than β-carotene. In conclusion, glycosyl carotenoids from the HU36 and GB1 Bacillus strains are readily bioavailable. This is due in part to their higher bioaccessibility but perhaps also due to their easier accumulation in tissues.