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<p>Hard-shelled foraminifera are protists able to build a calcareous or agglutinated shell (called a “test”). Here we study the impact of sediment acidification on calcareous test preservation. For this study, sediment cores were sampled in the macrotidal Auray estuary located on the French Atlantic coast. Living and dead foraminifera were quantified until 5 cm depth and discriminated using the Cell-Tracker™ Green vital marker. The pH and oxygen profiles combined with quantitative polymerase chain reaction (qPCR) suggested that cable bacteria were most likely to cause the acidifying process. Cable bacteria (CB) are filamentous bacteria coupling sulfide oxidation to oxygen reduction over centimetre distances, generating a strong pH gradient within the first few centimetres of the sediment that could affect the microhabitats occupied by benthic foraminifera. On two different intertidal mudflats, volumetric filament densities have been estimated. They were comparable to those observed in the literature for coastal environments, with 7.4 <span class="inline-formula">±</span> 0.4 and 74.4 <span class="inline-formula">±</span> 5.0 m cm<span class="inline-formula">⁻³</span> per bulk sediment, respectively. Highly contrasting sediment acidification (from low to very intense) was described from 1.0 to 2.4 <span class="inline-formula">Δ</span>pH. This seems to lead to various dissolution stages of the foraminiferal calcareous test from intact to fully dissolved tests revealing the organic lining. The dissolution scale is based on observations of living <i>Ammonia</i> spp. and <i>Haynesina germanica</i> specimens under a scanning electronic microscope. Furthermore, dead foraminiferal assemblages showed a strong calcareous test loss and an organic lining accumulation throughout depth under low pH, hampering the test preservation in deep sediment. These changes in both living and dead foraminiferal assemblages suggest that cable bacteria must be considered in ecological monitoring and historical studies using foraminifera as bioindicators and paleoenvironmental proxies.</p>