Across the eukaryotic tree of life, genomes vary within populations and within individuals during their life cycle. Understanding intraspecific genome variation in diverse eukaryotes is key to elucidating the factors that underlie this variation. Here, we characterize genome dynamics during the life cycle of Allogromia laticollaris strain CSH, a member of the Foraminifera, using fluorescence microscopy and reveal extensive variation in nuclear size and DNA content. Both nuclear size and DNA content are tightly correlated across a 700-fold range in cell volume. In contrast to models in yeast where nuclear size is determined solely by cell size, the relationship in A. laticollaris CSH differs according to both life cycle stage and food source. Feeding A. laticollaris CSH a diet that includes algae results in a 2-fold increase in DNA content in reproductive cells compared with a diet of bacteria alone. This difference in DNA content likely corresponds to increased fecundity, as reproduction occurs through segregation of the polyploid nucleus into numerous daughter nuclei. Environmentally mediated variation in DNA content may be a widespread phenomenon, as it has been previously reported in the plant flax and the flagellate Euglena. We hypothesize that DNA content is influenced by food in other single-celled eukaryotes with ploidy cycles and that this genome flexibility may enable these eukaryotes to maximize fitness across changing environmental conditions.