During processing of milk concentrates the microbiological load especially of thermophilic spore formers and their endospores may increase. Thus, not only the concentrate but also the thereof produced powder can contain high amounts of thermophilic spores that survive transport and storage and finally germinate upon reconstitution. High temperature treatments of milk concentrate prior to the evaporation process reduce the count of thermophilic spores (> 100 °C). However, such a treatment in the existing indirect heating plants is limited due to extended deposit formation, so called fouling. Only intensive cleaning procedures with heavy cleaning agents remove fouling from the plant. It is hypothesized that through the lack of hot walls continuous microwave heating of milk concentrates induces less fouling, retains the product properties, and diminishes the microbiological load of thermophilic spores. Skim milk concentrates (31.1 g/100 g dry matter, obtained via reverse osmosis) were heated in a continuously operated microwave heating plant in pilot scale (f = 2450 MHz, volume flow = 150 L/h). Temperatures ranging from 85 to 115 °C were applied with holding time t = 5 s. The concentrates were analyzed by means of L*a*b* colour space and particle size by static light scattering. Direct heating by microwave technology of skim milk concentrate within the designed process window was feasible, while product properties were maintained. Except yellowing of the samples, colour changes (browning) were not found. Particle formation was significantly reduced and low in comparison to indirect heating. The experimental results allow to set a process window for microwave heating of milk concentrates with minimal product changes. Thus, microwave technology presents a new method to heat fouling‑sensitive milk products.