This dataset (.crc and .cpr files) contain electron backscatter diffraction maps of thin sections of A. benedeni benedeni specimens SG-125, SG-126, and SG-127. Also included are .BMP files for each map. The bivalve shells were collected in 2013 from a shell bed at the top of the Oorderen Member of the Lillo Formation of the Pliocene in Belgium. The collection site was a construction-related temporary outcrop at the Deurganck Dock Lock (now Kieldrecht Lock) in the city of Antwerp, located at 51°16′44″N 4°14′52″E. These measurements were carried out in order to determine the microstructures of the shells of A. benedeni benedeni, as well as to screen for minor diagenetic alterations. The specimens were measured in spring 2021 at Department of Earth Sciences of Utrecht University, the Netherlands, on an Oxford Instruments Symmetry EBSD detector attached to a Zeiss Gemini 450 SEM. Thin sections of the samples were mechanically polished with 0.3 µm aluminium oxide suspension and finished with chemical Syton® polish. The thin sections were covered with a thin (several nm) carbon coating to keep charge build-up during the measurements at a minimum.