Symbiotic nitrogen- (N) fixing trees can influence multiple biogeochemical cycles by fixing atmospheric N, which drives net primary productivity and soil carbon (C) and N accumulation, as well as by mobilizing soil phosphorus (P) and other nutrients to support growth and metabolism. The soil micronutrient molybdenum (Mo) is essential to N-fixation, yet surprisingly little is known of whether N-fixing trees alter soil Mo cycling, and if changes to soil Mo are coupled to soil C, N, and P. We compared how symbiotic N-fixing red alder and non-N-fixing Douglas-fir trees modified surface soil C, N, P, and Mo across variation in climate and other site factors in the Pacific Northwest. We found that after two decades, N-fixing trees drove coupled increases in surface soil C, N, total P, and organic P. Consistent with contributions of N-fixing trees to soil organic matter, increased soil C and N were accompanied by lower δ13C in all sites, and lower δ15N in sites where non-fixer plots exhibited elevated soil δ15N. However, N-fixing trees did not affect surface soil Mo concentrations or fractions, suggesting that different factors control the cycling of P versus Mo over decadal timescales. Random forest analysis revealed that surface soil P was most strongly influenced by factors related to soil C accumulation, whereas surface soil Mo was related primarily to environmental factors, including potential differences in atmospheric Mo deposition across sites. Ratios of surface soil P:Mo were higher in extractable pools than in total soil digests, reinforcing the idea of stronger biotic cycling of P than Mo. Overall, our multi-site, multi-decadal field study found surprisingly small effects of N-fixing trees on soil Mo, despite rapid increases in soil organic C, N, and P. We hypothesize that, rather than direct effects of N-fixing vegetation, abiotic or indirect biotic factors such as soil sorption of atmospheric Mo inputs can link C–N–P–Mo cycles in terrestrial ecosystems on longer timescales.