Whey protein pectin complexes can be applied to replace fat in food products, e.g., pudding and yogurt, contributing to creaminess while adding a source of protein and fiber. Production of these complexes is usually conducted on the laboratory scale in small batches. Recently, a process using a scraped-surface heat exchanger (SSHE) has been employed; however, dispersion preparation time, feasibility of using different whey protein sources and enrichment of the complexes for subsequent drying have not been assessed. Preparing whey protein pectin dispersions by solid mixing of pectin and whey protein powders resulted in larger complexes than powders dispersed separately and subsequently mixed after a hydration time. Dispersions without hydration of the mixed dispersions before thermomechanical treatment had the largest particle sizes. The targeted particle size of d90,3 < 10 µm, an important predictor for creaminess, was obtained for five of the six tested whey protein sources. Dispersions of complexes prepared using whey protein powders had larger particles, with less particle volume in the submicron range, than those prepared using whey protein concentrates. Efficiency of complex enrichment via acid-induced aggregation and subsequent centrifugation was assessed by yield and purity of protein in the pellet and pectin in the supernatant.