Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MSⁿ) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MSⁿ process, both protonated and metal-cationized isariins generated product ions belonging to the identical ‘b-ion’ series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the ‘b’ or/and the ‘y’ ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the ‘y-type’. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.