This study aimed to evaluate the effects of conventional heat treatments (high‐temperature–short‐time and low‐temperature–low‐time) and high‐intensity ultrasound (HIUS) on the physical stability and bacterial diversity of whole milk during refrigerated storage. HIUS processing used an energy density of 3 kJ/mL and an ultrasound intensity of 90 W/cm2. The most abundant bacterial genera found in raw milk were Acinetobacter and Pseudomonas. After processing and storage for 7 days, Acinetobacter, Kluyvera and Serratia were the dominant genera in almost all samples, and Pseudomonas was the most abundant in HIUS‐processed milk. Only the HIUS process reduced the fat droplet size (<1 µm), providing better physical stability during the storage period. [ABSTRACT FROM AUTHOR]