Display omitted •pH 2 and pH 3.5 amyloid aggregate solution differ in their polydispersity.•Mixtures of amyloid and non-amyloids were compared with separated fractions.•Separated amyloid fractions differ in size and charge properties.•Separation reduced superposition effects for FTIR, Trp fluorescence and ThT analysis. It is well known that amyloid beta-lactoglobulin (BLG) fibril solutions contain a heterogeneous mixture of amyloid aggregates and non-amyloid material. However, few information are available on how strongly separated fractions of different morphologies (straight fibrils at pH 2 and worm-like aggregates at pH 3.5) vary with respect to physicochemical properties and building blocks as most analyses are conducted with unfractionized solutions where superposition effects occur. The pH-value shift resulted in an altered degree of acid hydrolysis which led to dissimilar building blocks of the aggregates (peptides at pH 2, non-hydrolyzed protein at pH 3.5). The respective separated amyloid and non-amyloid fractions showed significantly different size (SAXS, SEC, AUC) and charge properties (Zeta potential) than the whole samples. Strong superposition effects were evident with common analyses such as FTIR, TRP fluorescence and Thioflavin-T. At the same time, structural differences of pH 2 and pH 3.5 aggregates could be presented more clearly.