Summary Arbuscular mycorrhizal (AM) fungi are the most abundant plant symbiont and a major pathway of carbon sequestration in soils. However, their basic biology, including their activity throughout a 24‐h day : night cycle, remains unknown. We employed the in situ Soil Ecosystem Observatory to quantify the rates of diurnal growth, dieback and net productivity of extra‐radical AM fungi. AM fungal hyphae showed significantly different rates of growth and dieback over a period of 24 h and paralleled the circadian‐driven photosynthetic oscillations observed in plants. The greatest rates (and incidences) of growth and dieback occurred between noon and 18:00 h. Growth and dieback events often occurred simultaneously and were tightly coupled with soil temperature and moisture, suggesting a rapid acclimation of the external phase of AM fungi to the immediate environment. Changes in the environmental conditions and variability of the mycorrhizosphere may alter the diurnal patterns of productivity of AM fungi, thereby modifying soil carbon sequestration, nutrient cycling and host plant success.