During isolation, exopolysaccharides (EPS) from lactic acid bacteria are subject of thermal, chemical, enzymatic or ultrasound stress of different intensity that may affect macromolecular properties, for instance molecular mass or (intrinsic) viscosity. These parameters are, however, crucial, as they are associated with the technofunctional potential of EPS replacing commercial thickeners in nonfermented products. The aim of this study was to systematically examine treatments EPS are usually exposed to during isolation and to investigate the underlying degradation mechanisms. Solutions (1.0 g/L) of EPS from Streptococcus thermophilus, isolated as gently as possible, and commercial dextran were analyzed for molecular mass distributions as representative measure of molecule alterations. Generally, acid, excessive heat and ultrasonication, intensified by simultaneous application, showed EPS degradation effects. Thus, recommendations are given for isolation protocols. Ultrasonic degradation at 114 W/cm² fitted into the random chain scission model and followed third-(S. thermophilus EPS) or second-order kinetics (dextran). The degradation rate constant reflects the sensitivity to external stresses and was DGCC7710 EPS > DGCC7919 EPS > dextran > ST143 EPS. Due to their exceptional structural heterogeneity, the differences could not be linked to individual features. The resulting molecular mass showed good correlation (r² = 0.99) with dynamic viscosity.