Seagrass meadows are considered as potential blue carbon ecosystems through burial and long-term storage of organic carbon in their sediments. However, this climate benefit may be reduced or even negated by emissions of greenhouse gases (GHG) such as methane (CH₄) and nitrous oxide (N₂O). Here, we quantified seasonal CH₄ and N₂O fluxes and identified controlling biogeochemical factors in a shallow, sandy <em>Zostera marina</em> meadow (<em>Z. marina</em>) and an adjacent unvegetated site (Sand) in Denmark. We used in situ benthic chamber incubations under dark and light conditions, combined with measurements of plant biomass, porewater chemistry, solid-phase sediment variables, and ²¹⁰Pb concentration profiles. Fluxes of CH₄ were low overall, ranging from -0.8 to 15.5 &micro;mol m^-2 h^-1, with the largest emissions occurring in autumn. Across sites and seasons, CH₄ fluxes increased with <em>Z. marina</em> belowground biomass and decreased with the porewater NO_x (= NO₂^- + NO₃^-) inventories, indicating that root/rhizome-derived organic matter fueled methanogenesis, while more oxidizing conditions constrained net CH₄ release. In contrast, N₂O fluxes were small and variable (-0.44 to 0.32 &micro;mol m^-2 h^-1), without a clear seasonal pattern. The most important controllers of N₂O fluxes were light conditions and porewater NH₄⁺, suggesting a role for coupled or light-driven NO₂^-reduction and nitrification-denitrification processes. Sediment OC concentrations were uniformly very low (&lt; 0.4 %), and excess ²¹⁰Pb was restricted to the upper few centimeters without a consistent downcore decline, reflecting sediment mixing and suggesting low sedimentation rates, although neither these nor the OC sequestration rates could be quantified. Together with the negligible fine-sediment content, these results point to very limited long-term OC burial at this site. We therefore conclude that, in shallow organic-poor sandy sediments of <em>Z. marina</em> such as those studied here, even modest CH₄ emissions are sufficient to offset any likely climate-mitigation benefit from sedimentary carbon sequestration.