Microbioerosion structures are a common sign of microbial activity known mainly from marine environments and calcareous substrates, or from pollen records. However, the same phenomenon has been overlooked in animal fossils preserved in lake sediments. We studied 430 fragments of chitinous microfossils from three central European glacial lakes and detected microboring structures in approximately 10%. The microfossils belong to two size groups: (1) spherical objects with lengths ranging from 50 to 300 μm that are probably microturbelarian (Turbellaria: Rhabdocoela) cocoons, and (2) larger remnants (up to 2 mm long) of caddisfly (Insecta: Trichoptera) frontoclypeal apotomes. Four microbioerosion morphotypes were distinguished: (1) small holes (< 0.6 μm) oriented perpendicular to microfossil walls, likely produced by bacteria or fungi; (2) simple meandering tunnels and; (3) asterisk-like tunnel structures produced by fungi and/or fungus-like organisms; and (4) abrasions caused by biofilms. The maximum diameter of the simple holes and both tunnel structures depended on host-microfossil size: a higher diversity of microbioerosions was found on larger chitinous fragments. We propose that the good preservation of microfossils in the studied sediment samples might be due to rapid transport to the anoxic profundal zone or by rapid burial in anoxic sediments.