It has been postulated that endomyocardial fibrosis (EMF), a common cardiac disease in certain tropical communities including parts of Uganda, may be related to the presence of elevated levels of dietary Ce, and deficient levels of dietary Mg. In Uganda, significant variation in dietary exposure to both elements is likely due to variations in local soil geochemistry and dietary habits, including geophagia (the deliberate consumption of soil). This paper reports the concentration and bioaccessibility (determined from a physiologically based extraction test—PBET) of Ce and other essential (Mg and Fe) and trace elements in soils from the Mukono district of Uganda. Trace element concentrations varied markedly between soil samples (ground soils) and soils eaten deliberately, such as termite nest soils and traditional herbal–soil remedies. The highest bioaccessibility values were reported for the chelate-rich, intestinal phase of the PBET. Median percentage bioaccessibility values for Ce (1–15%), Mg (7–33%), Fe (0.1–2.9%) and other trace elements varied considerably, but were generally higher in geophagic (herbal–soil remedies and terminte nest soils) than common (ground) soil samples. Only in the case of Fe does the ingestion of soil account for a major proportion of recommended daily intake (RDI). The revised estimates of Ce and Mg dietary intake (based on bioaccessibility data rather than an assumption of 100% bioavailability) significantly reduced the importance of geophagia relative to exposure through the ingestion of food and water.