Two major quality defects of yogurt are syneresis and the presence of large particles, and several reasons have been extensively discussed. Vibrations during fermentation, particularly generated by pumps, must be considered as a further cause as latest research showed that both ultrasound and low frequencies induced visible particles. The aim of this study was to investigate the impact of sonication during fermentation with starter cultures differing in exopolysaccharide (EPS) synthesis on the physical properties of set (syneresis, firmness) and stirred yogurt (large particles, laser diffraction, rheology). Skim milk was fermented with starter cultures YC-471 (low EPS) or YF-L 901 (high EPS) (Chr. Hansen) and sonicated for 5 min at pH 5.2. Sonicated set gels exhibited syneresis and were softer than respective controls. The mechanical treatment was adjusted to quantify visible particles (d ≥ 0.9 mm) in stirred yogurts properly. Sonication significantly increased particle numbers, however, the effect was less pronounced when YF-L 901 was used, indicating EPS as a tool to reduce syneresis and particle formation due to vibrations. Rheological parameters and size of microgel particles were rather influenced by starter cultures than by sonication.