Gluten-free products exhibit some undesirable features due to the absence of the gluten network. Effects of ingredient interactions and baking type on the food matrix have not clearly been explored. The objective of this study was to investigate the effect of ingredient and baking types on the quality characteristics of cake by using nuclear magnetic resonance (NMR) relaxometry. Carob bean flour containing gluten-free cakes formulated either with hydroxypropyl methylcellulose (HPMC) or whey protein were baked in both conventional and microwave-infrared combination ovens. Specific gravity of batters was measured and cakes were analyzed in terms of weight loss, hardness, and specific volume. Microstructure of cakes was investigated by scanning electron microscopy (SEM). NMR relaxometry was used to support the information about water retention, and water-food matrix interactions. Cakes baked in microwave-infrared (MW-IR) combination oven had some undesirable characteristics due to higher weight loss and insufficient gelatinization of stanch which was supported by SEM results. Compartments of relaxation data also indicated two specific proton pools for MW-IR-baked samples, which represented gelatinized and ungelatinized parts of the cakes. Spin-spin relaxation times (T-2) were found to be good indicators for explaining the physical state and distribution of water inside the samples, having Pearson correlation of 0.96, 0.86, and - 0.98 (p < 0.05) between monoexponential T-2 values and hardness, specific volume, and moisture, respectively.