Storage of selenium and iodine can greatly vary between forest ecosystems, but the influence of tree species on partitioning and recycling of those elements remains elusive. In this study, contents of Se and I were measured in tree compartments, litterfall, humus, and soil horizons in monospecific stands of Douglas fir, pine, spruce, beech, and oak under identical climatic and edaphic conditions. The cycle of each element was characterized in terms of stocks and fluxes. Lowest concentrations were in wood (Se: 8–13 μg kg−1; I: <16.5 μg kg−1). Senescing organs had higher Se and I content, than the living parts of trees due to direct exposure to atmospheric deposition, with some variation between coniferous and deciduous trees. For all stands, low amounts of Se and I were involved in biological cycle as reflected by low root uptake. In humus, the enrichment of elements greatly increased with the stage of organic matter (OM) degradation with average factors of 10 and 20 for Se and I. OM degradation and element persistence in humus was influenced by tree species. Deciduous trees, with low biomass, and fast degradation of OM stored less Se and I in humus compared to fir and spruce with high humus biomass. Interestingly, tree species did not affect soil reserves of Se and I. Concentration ranges were 331–690 μg Se kg−1 and 4.3–14.5 mg I kg−1. However, the divergent vertical profiles of the elements in the soil column indicated greater mobility of I. Selenium concentrations regularly decreased with depth in correlation with OM and Fe oxides content. For iodine, the maximum iodine concentration at a soil depth of 15 to 35 cm was caused by a parallel precipitation/sorption behavior of aluminium and organic iodine dissolved in the topsoil.