We investigated Quaternary benthic foraminifera in core GPC1803 in the eastern equatorial Indian Ocean since ~740 ka to examine the relationship between benthic foraminiferal fauna and ballasting of particulate organic matter (POM) by calcareous plankton skeletons. Because plankton skeletons affect POM sinking in the water column as ballasts, ballasting of POM by biominerals may play an important role to linkage between the surface and deep-sea paleoceanography. We consider this scheme, based on faunal analysis of benthic foraminifera. From multidimensional scaling (MDS) of fossil benthic foraminifera, we recognized two MDS axes. Based on the scores of MDS axis 1, we subdivided our study period into five intervals and identified two major faunal transitions at ~370 ka and ~ 210 ka. After ~210 ka, the food supply to the seafloor increased with an increase in the past flux of calcareous plankton skeletons. A positive correlation between the benthic foraminifera accumulation rate and the carbonate mass accumulation rate existed during ~600–370 ka and after ~210 ka. It is reasonable to suppose that the increase in calcareous plankton skeletons stimulated more efficient vertical transport of POM through the water column due to the positive ballasting effect on POM. The ~370–210 ka period seemed to represent a transitional phase in food supply. Prior to ~370 ka, alternations among three seasonal food supply-related species were generally observed along with glacial–interglacial variations probably under lower food supply, compared with the after ~210 ka period; however, alternations among these three species became obscure and intermittent after ~370 ka. The nearly continuous common occurrences of these seasonal food supply-related species before ~370 ka might have been enhanced by a lower past flux of calcareous plankton skeletons. Scenario of ballasting of POM by biomineral might explain long-term changes of carbonate corrosivity in the Indian Ocean, similarly in the Atlantic and eastern equatorial Pacific Oceans, during the mid-Brunhes dissolution interval. • Quaternary deep-sea benthic foraminifera in the equatorial Indian Ocean • Positive relationship between BFAR and carbonate MAR after ~210 ka • Common occurrences of seasonal food supply-related species before ~370 ka • Changes in the influence of ballasting of POM by calcareous plankton