The nutrient and carbon (C) allocation dynamics in mycorrhizal hyphal networks cause variation in costs and benefits for individual plants and fungi and influence the productivity, diversity and C cycling in ecosystems. We manipulated light and phosphorus (P) availability in a pot experiment with Trifolium subterraneum colonised by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. Stable 13C-labelling was used to trace assimilated CO2 to the mycorrhizal fungus in roots and soil using compound-specific isotope ratio mass spectrometry. We used the neutral lipid fatty acid 16:1ω5 as a signature for AM fungal storage lipids. Both P and shading reduced the AM fungal lipid accumulation in the intraradical mycelium, while only P reduced the amount of lipids in the extraradical mycelium. Recently assimilated plant C was only allocated to the mycorrhizal fungus to a small extent when plant mycorrhizal benefit was reduced by P fertilization, while increasing the plant C cost by shading did not reduce the C flow to the fungus. These results are of importance for our conception of mycorrhizal dynamics during periods of shade in nature.