Novel stable BODIPY boron mono- and diperoxides were prepared in good yields by TMSOTf activation of mono- and dialkoxy-BODIPY derivatives, followed by ligand exchange with organic hydroperoxides. The reactions of the methoxy derivative of BODIPY with hydroperoxides led to the formation of a novel group of peroxides with the structural element B(F)OOR. The reaction of the dimethoxy derivative of BODIPY with tBuOOH provided the first organic boron diperoxide. Using gem-dihydroperoxide, a cyclic analogue with tetraoxaborinane ring was prepared. Both, mono- and diperoxo boron compounds are stable under ambient conditions, which allowed full characterization of compounds. A mechanistic study provided further insight into their formation and elucidated some of the possible intermediates, namely the borenium cations.