A customized phase treatment (CPT) process to produce shelf-stable milk with high native whey protein and vitamin contents, and at the same time low plasmin activity was developed. Therefore, skim milk was microfiltered (pore size 0.1 μm) and the obtained retentate was ultra-high temperature (UHT, ϑ = 140 °C, t = 5 s) heated with long pre-heating (ϑ = 95 °C, t = 128 s) while the permeate was microwave heated to 120 °C for 5 s. After sterile mixing and filling the milk was compared to indirectly and directly processed UHT milk. CPT milk resulted in whey protein denaturation, lactulose formation, and thiamine loss ranging in-between direct and indirect UHT milk. CPT and indirectly heated UHT milk had comparable shelf-lives, while direct steam injection resulted in reduced shelf-life with particle formation, sedimentation, and age-gelation accompanied by increased apparent plasmin activity over storage. This study highlights the potential of CPT aiming to achieve eco-friendly and high-quality dairy processes and products. • Novel process for shelf-stable milk: Customized phase treatment (CPT). • CPT uses microfiltration and separate heating of milk, involving microwave heating. • Storage (20 & 30 °C) and evaluation of CPT, directly and indirectly heated UHT milk. • Kinetic modelling of time-temperature integrators. • CPT milk has equal shelf-life with improved quality compared to indirect UHT milk.