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• The induction, growth and maturation of Begonia somatic embryos were changed under MG. • MG influenced SE through altering endogenous hormone biosynthesis and energy metabolism. • Energy metabolism was the key for high frequency SE induction under clinorotation. • An increase in biomass and chlorophyll content in response to MG was observed. • Long-term exposure to MG promoted somatic embryo maturation, induced stomatal morphological distortion. The present study provides a visual insight into the effects of simulated microgravity (MG) on somatic embryogenesis (SE) in Begonia through the analysis of phytohormone fluctuations and energy metabolism. To investigate this relationship, thin cell layer culture model was first used. The results showed that MG changed the phytohormone content and stimulated starch biosynthesis to convert into sugar to release energy needed for regeneration and proliferation. Moreover, from the results it is likely that MG accelerated the initiation and subsequently maturation and aging of SE via decrease of AUX and increase of ABA. High content of GA, CKs, starch, sugar and low ABA as well as high CKs/ABA ratio were responsible for the increase in the number of embryos under clinorotation which was 1.57-fold higher than control after 90 days. The increase in fresh and dry weight of somatic embryos and chlorophyll content under MG were confirmed as their adaptive responses to gravitational stress. However, long-term exposure to MG (120 days) stimulated biosynthesis of ABA levels 1.85-fold higher than controls, which resulted in a decrease in chlorophyll content, increase in number of mature embryos and stomata length. These results revealed that MG regulated the induction, differentiation and senescence of somatic embryos via a biochemical interaction pathway. [ABSTRACT FROM AUTHOR]