Large benthic foraminifera are significant contributors to sediment formation on coral reefs, yet they are vulnerable to ocean acidification. Here, we assessed the biochemical and morphological impacts of acidification on the calcification of
Amphistegina lessonii
and
Marginopora vertebralis
exposed to different pH conditions. We measured growth rates (surface area and buoyant weight) and Ca-ATPase and Mg-ATPase activities and calculated shell density using micro-computer tomography images. In
A. lessonii
, we detected a significant decrease in buoyant weight, a reduction in the density of inner skeletal chambers, and an increase of Ca-ATPase and Mg-ATPase activities at pH 7.6 when compared with ambient conditions of pH 8.1. By contrast,
M. vertebralis
showed an inhibition in Mg-ATPase activity under lowered pH, with growth rate and skeletal density remaining constant. While
M. vertebralis
is considered to be more sensitive than
A. lessonii
owing to its high-Mg-calcite skeleton, it appears to be less affected by changes in pH, based on the parameters assessed in this study. We suggest difference in biochemical pathways of calcification as the main factor influencing response to changes in pH levels, and that
A. lessonii
and
M. vertebralis
have the ability to regulate biochemical functions to cope with short-term increases in acidity.