<p>Shrubland ecosystems play a crucial role in Mediterranean forests, contributing to soil protection, biodiversity conservation, carbon sequestration, and ecosystem restoration. In semi-arid regions, mycorrhizal woody plants such as <i>Helianthemum</i> spp. form ectendomycorrhizal symbiosis with edible desert truffles, representing an emerging and sustainable crop with significant potential for rural development and economic diversification. Significant progress has been made in the breeding of <i>Terfezia claveryi</i> Chatin, but key aspects of its life cycle, such as the temporal and spatial behaviour of the soil mycelium, remain underexplored. This study aimed to investigate the seasonal dynamics of <i>T. claveryi</i> soil mycelium in plantations and wild areas of the Region of Murcia (Spain) using real-time quantitative PCR. The relationship between fungal biomass and host plant phenology and environmental parameters was also investigated. Our results showed that <i>T. claveryi</i> soil mycelium was higher in plantations than in wild areas, and in Xerolls than in Orthents soils. Fungal dynamics lacked seasonal or annual patterns; however winter mycelium showed a strong correlation with preceding agroclimatic variables, especially precipitation and maximum temperature. This research sheds light on the ecological processes underlying the desert truffle shrublands and offers practical implications for optimising <i>T. claveryi</i> cultivation strategies and promoting ecosystem restoration.</p>