This study investigated the effects of elevated temperature on shell density and Mg-ATPase activity of Amphistegina lobifera. This species is abundant in shallow reef habitats, and can be vulnerable to daily physicochemical fluctuations. To assess potential responses and acclimation mechanisms of A. lobifera to changing temperature conditions, we performed a blocked-design experiment exposing specimens collected from different reef sites (inshore and offshore) to three temperature treatments (Control: 24 °C, + 2 °C: 26 °C and + 5 °C: 29 °C) for 30 days. The final size and shell density of inshore reef foraminifera were unaffected by elevated temperature, and the enzyme activity in these individuals showed that they were able to acclimate to new temperature conditions. In contrast, offshore A. lobifera were more sensitive to changes in temperature, and heat stress caused growth impairment and inhibited Mg-ATPase activity. However, newly added chambers were not affected. These results suggested that Mg-ATPase plays an important role in regulating intracellular Mg ions, but has little influence in the onset of calcification in A. lobifera. Moreover, it suggests that even though A. lobifera can regulate intracellular functions, local habitat seems to play a crucial role in determining how foraminifera respond to environmental changes.