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Carotenoids are accessory photosynthetic pigments used as natural antioxidants, safe colorants, and nutraceuticals. Microalgae are the richest biotechnological source of natural carotenoids. Microalga Bracteacoccus aggregatus strain IPPAS C-2045 isolated from the White Sea region responds to stresses, including high light, with carotenogenesis—gross accumulation of secondary carotenoids (the carotenoids structurally and energetically uncoupled from photosynthesis). Precise mechanisms of cytoplasmic transport and subcellular distribution of the secondary carotenoids under stress in are still unknown. Using B. aggregatus as a model with multimodal imaging combining micro-Raman imaging (MRI), fluorescent lifetime (τ) imaging (FLIM), and transmission electron microscopy (TEM), we monitored the ultrastructural and biochemical rearrangements of B. aggregatus cells during the stress-induced carotenogenesis. MRI revealed a decline in the diversity of molecular surrounding of the carotenoids (likely, relocation of the carotenoids from functionally and structurally heterohenous photosynthetic apparatus to the more homohenous lipid matrix of the oleosomes). Two-photon FLIM highlighted pigment transformation and re-distribution in the cell during carotenogenesis. The structures co-localized with the carotenoids with shorter τ (mainly chloroplast) shrunk whereas the structures harboring secondary carotenoids with longer τ (mainly oleosomes) expanded considerably. Fluorescence of B.aggregatus carotenoids, either in situ or in acetone extracts, possessed surprisingly long lifetime. We hypothesize that the extension of τ of the carotenoids can be due to their aggregation and/or association with lipids and specialized proteins. The propagation of the Car species with prolonged τ is considered to be a manifestation of the secondary carotenogenesis which can be employed for its non-invasive monitoring with multi-modal imaging.