Plant secondary metabolites (PSMs) play an important role in plant defense, and their patterns of inheritance may help explain the varying susceptibility of plant hybrids to herbivore and pathogen pests. Here, we studied the inheritance of PSMs in artificial hybrids between two temperate plantation species, Eucalyptus globulus and E. nitens, growing in a common environment field trial. Six different cross-types were compared: both pure species, F1, F2 and both backcross classes. We sampled 190 13-year-old trees and assayed adult foliage for nine different PSM components: condensed tannins, total phenolics, total oils, 1,8-cineole, α-pinene, aroma-dendrene, β-eudesmol, sideroxylonal A and macrocarpal G. We found significant variation between the six cross-types for all but one compound (β-eudesmol). While discriminant analysis shows the hybrids are generally intermediate in their chemical profile, the overall inheritance of the chemical differences between the two eucalypt species was non-linear due to the non-additive inheritance of many compounds. The inheritance of five of the nine PSMs studied exhibited significant deviations from additivity in the F1’s. Specifically, all hybrid classes had greater levels of sideroxylonal A and condensed tannins than either pure species suggesting heterosis; a relatively uncommon pattern of inheritance in PSMs. This increased expression of PSMs in the hybrids may have implications for the development of pest management approaches in planted forests for commercial or restoration purposes.