Phosphonate peptides were synthesized and investigated by positive ion electrospray ionization mass spectrometry in conjunction with tandem mass spectrometry. It was found that, for the sodiated adduct, there were two rearrangement reactions. In path A, there was C-C covalent bond cleavage with consecutive migration of a hydrogen atom to lose the amino alcohol molecule. In path B, two consecutive covalent cleavages of the C-N and P-O bonds occurred.