Proteins acting as powerful inhibitors of plant pectin methylesterase and polygalacturonase were isolated from whole lemon fruits (Citrus limon L.). Pectin methylesterase inhibitor (PMEI) and polygalacturonase inhibitor protein (PGIP) were purified using DEAE Sepharose column, resulting in fold purity of 89.13 and 81.16 and having a molecular mass of 35 and 38 kDa, respectively as estimated using SDS-PAGE and MALDI-TOF mass spectroscopy. The optimum pH of purified PMEI and PGIP was pH 6 and pH 4.5 while the inhibitors showed good stability in the pH range of 5–8 and 3.5 to 5.5, respectively. Both the inhibitors from C. limon demonstrated an optimum temperature of 55 °C. Thermal inactivation data suggested that purified PGIP was more heat stable than PMEI. The inhibition kinetics of PMEI and PGIP towards C. limon PME and C. limon PG was of a non-competitive type. Both PMEI and PGIP obeyed first-order inactivation kinetics. The PMEI and PGIP exhibited different extent of inhibition towards PME and PG from other fruit sources analyzed in this study. As these inhibitors inhibit PME and PG from other plant sources they can be used in fruit-based products to control undesirable endogenous enzyme activities as an alternative to thermal processing.