An important question in climate modeling is whether carbon cycling is fundamentally different in warm versus cold climate states. A key line of evidence regarding this question comes from the unusually large difference in carbon-isotope values (δ13C) between shallow-dwelling muricate foraminifera and foraminifera living deeper in the water column in the Paleogene. This has been interpreted as evidence that warmer temperatures elevated the metabolic rates of carbon-recycling bacteria, resulting in a steeper gradient in the δ13C of dissolved inorganic carbon (δ13CDIC) and reduced carbon export. However, this interpretation depends on the assumption that vital effects—biological processes that bias foraminiferal δ13C—are constant throughout time. We test this assumption using a chemical model of the foraminiferal microenvironment and find that the hypothesized increase in metabolic rates should also increase vital effects, meaning that both Paleogene δ13CDIC gradients and the temperature dependence of metabolism must have been significantly lower than previously estimated. We further propose that muricate foraminifera may have evolved a novel “mat” strategy for photosymbiosis wherein symbionts rested on the muricae in a thin layer surrounding the shell. This hypothesis can explain both the function of muricae and the observed isotopic data without the need for any change in metabolism. Our work thus challenges existing interpretations of δ13C and provides a path forward to empirically test the magnitude of temperature-dependent metabolic change in the deep past.