The physiological changes in the intertidal benthic foraminiferal species Ammonia confertitesta were described using the mean fluorescence intensity (i.e., Nile Red, Acridine Orange and Cell-ROX fluorogenic probes) under confocal microscopy, after exposure to oil-spiked (Macondo crude oil) sediments at three different concentrations (0, 0.044, and 0.44 g/cm3) and three time points (24, 48, and 72 h). The physiological changes are associated with an intracellular accumulation of neutral lipids (i.e., lipid droplets), a proliferation of acid vesicles (i.e., lysosomes), and enhanced production of reactive oxygen species (ROS) (i.e., oxidative stress). Statistically significant differences (Kruskal-Wallis H and Mann Whitney U; p < 0.001) are observed between concentrations, with the highest production of lipid droplets and ROS occurring at 0.44 g/cm3 across the time points. However, the highest lysosome production occurs at 0.044 g/cm3. The increased number of lipid droplets and lysosomes are a detoxifying strategy where oil may be sequestered and biologically inactivated via hydrolytic enzymes, that are responsible for digesting biomolecules. However, the free radical production, as evidenced by increased ROS mean fluorescence intensity, most likely leads to cellular damage. Overall, the observed physiological alterations observed support how effective and reliable benthic foraminifera are as proxies of environmental stress.