Due to their fast precipitation rate, sulfate evaporites represent excellent repositories of past life on Earth and potentially on other solid planets. Nevertheless, the preservation potential of biogenic remains can be compromised by extremely fast early diagenetic processes. The upper Miocene, gypsum‐bearing sedimentary successions of the Mediterranean region, that formed ca. 6 million years ago during the Messinian salinity crisis, represent an excellent case study for investigating these diagenetic processes at the expense of organic matter and associated biominerals. Several gypsum crystals from the Northern Mediterranean were studied by means of destructive and non‐destructive techniques in order to characterize their solid inclusion content and preservation state. In the same crystal, excellently preserved microfossils coexist with strongly altered biogenic remains. Altered remains are associated with authigenic minerals, especially clays. The results demonstrate that a significant fraction of organic matter and associated biominerals (notably biogenic silica) underwent early diagenetic modification. The latter was likely triggered by bottom sulfidic conditions when the growth of gypsum was interrupted. These results have significant implications for the interpretation of the Messinian Salt Giant.