Cold-seep carbonate concretions were preserved in the Chiahsien paleoseep remnant within the Pliocene Yenshuiken Formation of southwestern Taiwan foreland sequence. Compared to the non-seep controls in the Yenshuiken Formation, muddy host rocks that were <30 cm from massive authigenic carbonate concretions (ACCs) have low CaCO3 contents (~1%), high percentages of agglutinated foraminifera (~90%), and almost no calcareous foraminifera (both benthic and planktonic). However, host rocks that were >30 cm away from such ACCs have normal marine assemblages (low agglutinated foraminifera percentages, <6.6%; fair CaCO3 content, 3.5–7.9%). Host rocks that were <80 cm from chimney-shaped ACCs also have abnormal assemblages, whereas those >80cm away from the chimneys have normal assemblages. Host rocks between pipe-shaped ACCs have similar characteristics to mudstone samples from control sites. Low percentages of calcareous foraminiferal fossils in the paleoseep remnant are due to pore wateracidification within the taphonomically active zone (TAZ), which is triggered and accelerated by oxidation of sulfide (HS-, the product of anaerobic oxidation of methane [AOM]) in the methane seep environments. We suggest that foraminiferal assemblages can be influenced by methane seep activities taphonomically and that, therefore, ratios between calcareous and agglutinated foraminifera can reflect and record geochemical interface (e.g., TAZ; sulfate–methane interface [SMI] where AOM occurs) shifts on a subtler scale (only few decimeters) in paleoseep remnants.