As interaction between proteins and polysaccharides is expected to change the average diffusion coefficient and the distribution width, it is believed that NMR diffusometry can be a useful tool to study and quantify the interaction between whey protein isolate (WPI) and low methoxyl pectin (LMP). For this purpose, the influence of pH, dry‐heat‐treatment duration, and WPI to LMP ratio on WPI and LMP interaction was evaluated using pulsed field gradient NMR. At pH 5.0 and 5.5, approximately 40–50% of the WPI present in the mixture interacted with LMP through electrostatic interaction. Hence, it is important to measure the degree of covalent interaction at a pH where electrostatic interaction between WPI and LMP is limited. The diffusion coefficient of WPI gradually decreased as the mixtures of WPI and LMP were incubated for 1, 2, 8, and 16 days, which was accompanied by an increase in the distribution width. With regard to the LMP concentration, the higher the LMP concentration, the higher the amount of WPI bound to LMP and the smaller the diffusion coefficient of WPI. Overall, the results indicate that NMR diffusometry enables the quantification of the interaction in biopolymer mixtures. Whereas the results showed a similar trend as that obtained via chemical analysis, pulsed field gradient NMR does not require any sample pretreatment.