The effects of the temperature on the multi-exponential transverse relaxation signal of fruit tissues were studied by MRI at 1.5 T, with tomato as an example of fleshy fruits. The relative importance of chemical exchange mechanisms was investigated by comparing the results obtained from tomatoes with those obtained from aqueous solutions made up to simulate the vacuolar water pool. A more extended analysis of the effects of chemical exchanges on transverse relaxation time distributions was performed using the two-site Carver and Richards’s expression, by fitting the experimental dispersion curves with the theoretical model. At temperatures between 7 and 32 °C, the transverse relaxation signal in tomato pericarp was multi-exponential, indicating that cell membranes acted, at least partially, as barriers to diffusive exchanges of water molecules between cell compartments. Unexpectedly, the transition from two to three peaks in the T2 distribution occurred between 7 and 15 °C for most of the tomatoes analyzed. Further, the relaxation time of the vacuolar water pool of the tomato pericarp remained mostly stable with temperature, which was contrary to expectations when only chemical exchange mechanisms were taken into account. It was deduced that additional mechanisms compensated for the expected increase in T2 in the tomato pericarp. The hypotheses were discussed, in which the loss of the water magnetization at the membranes was assumed to be produced either by diffusive exchanges between compartments or by chemical exchanges between protons from water molecules and solid membranes.