A fresh baby puree (FP) was elaborated with quinoa and amaranth flours (native and germinated), and the nutritional, technological, and sensory changes induced by different drying methods were investigated: lyophilization (LD), forced convection (CD), and extrusion (ED). FP had an amino acids content appropriate for baby consumption; ED had lower digestibility (75%) compared with CD (82%) and LD (83%). ED had the highest water absorption capacity (2.2 g/g). Rehydrated LD had the lightest color (L* = 67), while rehydrated ED (L* = 59) was the darkest. Rehydrated ED had the highest hardness (335 N), adhesiveness (1199 N.m), and chewiness (209 N). Both rehydrated LD and CD were described as having an intense, bitter, and strange flavor; while rehydrated ED was described as dark, consistent, sweet, fruity, and presented the best acceptability. Therefore, the appropriate method to obtain dehydrated baby purees was extrusion. Novelty impact statement Babies are a vulnerable age group because they have an underdeveloped digestive system; therefore, the use of nutritionally improved foods, such as those obtained from germination, could give added value to the products developed for them. In this study, the characteristics of a gluten-free baby puree formulated with germinated Andean grains were highlighted; furthermore, as the dehydration could increase the shelf life and availability of the puree, it was dried by different methods. The rheological, textural, and sensory characteristics of the rehydrated puree were studied, leaving for later publications the study of the generation of anti-nutritional or toxic compounds during drying.