The relationship between the structural and functional changes of the photosynthetic apparatus in the flower bud of Lilium longiflorum during chloroplast–chromoplast transition was examined. Compared with green petals, there was a five-fold increase of the carotenoid content in yellow petals, whereas the chlorophyll content decreased five-fold. Absorption and emission fluorescence spectra of chromoplasts indicated that newly synthesized carotenoids were not associated with photosystem II (PSII) photochemistry. The maximum quantum yield in the remaining PSII reaction centers remained constant during the chromoplast formation, whereas the photosynthetic electron transport beyond PSII became inhibited, as indicated by a marked decrease of the O₂ evolution capacity, of the photochemical quenching of chlorophyll-a fluorescence and of the operational quantum yield of photosynthetic electron transport. Deconvoluted fluorescence emission spectra indicated a more rapid degradation of photosystem I (PSI) complexes than of PSII during chromoplast formation. Compared with green petals, the spillover between PSII and PSI decreased by approximately 40% in yellow petals. Our results indicate that during chloroplast–chromoplast transition in the flower bud of L. longiflorum, PSII integrity was preserved longer than the rest of the photosynthetic apparatus.