This study describes the use of Nuclear Magnetic Resonance (NMR) relaxometry to understand the effect of pectin methyl esterase (PME) + CaCl2 infusion under different conditions on cell integrity of fresh-cut and frozen–thawed mangoes. Infusion experiments were performed at: atmospheric pressure, vacuum conditions of 50 kPa and 10 kPa. For NMR relaxometry experiments T2 (spin–spin relaxation time), T1 (spin–lattice-relaxation times) and 2D T1–T2 experiments were performed. Results showed that, as the severity of the vacuum treatment increased, the relaxation times changed significantly (p < 0.05). The number of compartments observed in 1-D relaxation spectra of fresh and frozen–thawed mangoes changed with different treatments. The changes in relaxation times were explained due to formation of a gel formed by the interaction of pectin and calcium. 2D T1–T2 relaxation maps showed that compartmentalization was retained after vacuum treatment even for frozen–thawed samples. The study showed that NMR relaxometry is a useful tool to analyze the cell integrity of mangoes exposed to different treatments.