Background and Aim Climate change models are limited by lack of baseline data, in particular carbon (C) allocation to - and dynamics within - soil microbial communities. We quantified seasonal C-assimilation and allocation by plants, and assessed how well this corresponds with intraradical arbuscular mycorrhizal fungal (AMF) storage and structural lipids (16: 1 omega 5 NLFA and PLFA, respectively), as well as microscopic assessments of AMF root colonization. Methods Coastal Hypochoeris radicata plants were labeled with (CO2)-C-13 in February, July and October, and C-13-allocation to fine roots and NLFA 16: 1 omega 5, as well as overall lipid contents and AM colonization were quantified. Results C-allocation to fine roots and AMF storage lipids differed seasonally and mirrored plant C-assimilation, whereas AMF structural lipids and AM colonization showed no seasonal variation, and root colonization exceeded 80 % throughout the year. Molecular analyzes of the large subunit rDNA gene indicated no seasonal AMF community shifts. Conclusions Plants allocated C to AMF even at temperatures close to freezing, and fungal structures persisted in roots during times of low C-allocation. The lack of seasonal differences in PLFA and AM colonization indicates that NLFA analyses should be used to estimate fungal C-status. The implication of our findings for AM function is discussed.