Wet-mixing processes can be tuned to reduce energy consumption, although impacts on quality and stability should be addressed. This work evaluated the effect of wet-mix processing (total solids, TS: 50 or 60%; heat treatment: 75 or 100 °C × 18 s) and storage conditions (open package: 25 °C, 58% RH, 4 weeks; closed package: 25 °C, multilayer bag, 12 weeks) on the physicochemical stability and digestibility of infant formulas. Processing significantly influenced the physicochemical characteristics of the powders, with TS exerting a stronger impact than heat treatment. Powders produced from 60% TS wet mixes presented the fastest water sorption, which accelerated lactose crystallisation and fat liberation. Formulas in closed packages were stable for 12 weeks. While lactose crystallised before week 2 in open-package storage, inducing major physical changes, only limited effects were observed on digestibility. These findings provide valuable insights to ensure consistent quality during shelf-life of infant formula.