Abstract Coral skeletal trace‐metal compositions are commonly assumed to derive from seawater, yet the extent to which biological processes contribute remains poorly constrained. Here we present the first paired Mo isotope measurements of coral tissue, symbiotic zooxanthellae, and skeleton. All three compartments are depleted in δ98Mo relative to seawater, with zooxanthellae significantly lighter than host tissue. A strong negative correlation between zooxanthellae and skeletal δ98Mo, together with a negative power‐law relationship between skeletal Mo concentration and δ98Mo across species and reef environments, indicates a symbiont‐mediated control on Mo partitioning. Fossil corals further show systematic variability in skeletal δ98Mo associated with climate variability over the past millennium, suggesting that environmental changes modulate symbiont‐driven biological processes recorded in coral skeletons. These observations suggest that biologically processed Mo contributes substantially to skeletal composition and that coral δ98Mo may serve as a novel proxy for symbiont metabolic activity and its response to environmental change.