In this data set, we present the low carbonate ion condition in the deep sea region of the central Equatorial Indian Ocean (5°N & 77°E) over the last 40ka. The marine sediment core SSD044_GC-01 was collected during the 044th Cruise of RV Sindhu (SSD044) Sadhana using a Gravity corer. The age model of the core was obtained using four accelerator mass spectrometry (AMS ) 14C dates on ~15 mg of mixed planktic foraminiferal species, viz, Globigerinoides ruber, Globigerinoides sacculifer, Neogloboquadrina dutertrei and Globorotalia menardii. The radiocarbon dates were calibrated to calendar ages using the calib 7.1 programme (Reimer et al., 2013). For the analysis of shell weights of selected planktic foraminifera, a portion of the Coarse Fraction was adequately cleaned and sonicated. The >63 μm residue was dry sieved between 300 and 355 μm size fractions. Fifty tests of G. ruber, P. obliquiloculata, and N. dutertrei were picked and weighed on a microbalance (1σ precision: ± 2 μg, n =10). Shell weights of selected planktic foraminifera (G. ruber, P. obliquiloculata, N. dutertrei) show a low carbonate ion concentration in the deep sea region of the study area.