The electron impact ionisation (EI) and electrospray ionisation (ESI) mass spectra using in-source collision-induced dissociation of nine different cinchona alkaloid derivatives [iso-cinchona alkaloids (ethereal isomers) and 10-Br(Cl) containing cinchona compounds] have been studied. In the case of the EI method for iso-cinchona alkaloids the observed fragmentation directions are as follows: isomerisation of the cyclic ethers to the corresponding C9 ketone, the formation of [M − 15]+, [M − 29]+ and [M − 57]+ fragments as a result of the loss of methyl, ethyl and butyl radicals, and the cleavage of the C8–C9 bond. The fragmentation of the compounds containing C10–Br(Cl) bonds started with the scission of this bond. The primary bond rupture is followed by the fragmentation of the primary product into two parts across the C8–C9 bond. In the case of the ESI method at low capillary exit voltage only the peak of the protonated molecule ([M + H]+), and in a significantly lower abundance, the peak of the [M + 2H]2+ ion can be observed. Increasing the capillary exit voltage causes fragmentation to occur. For iso-cinchona alkaloids the main direction is the cleavage of C8–C9 bond. For the C10–Br(Cl) compounds, the primary fragmentations are the cleavage of the C9–O and C10–Br(Cl) bonds. Fragmentation pathways are discussed.