Carbon (C) in soils accounts for a substantial and dynamic portion of the global C cycle, with concentrations of soil organic carbon (SOC) typically closely linked to vascular plant productivity. However, C fixed by non-vascular photosynthetic organisms may account for a sizeable proportion of SOC in locations where vascular plants are not abundant. In the hyperarid Namib Desert, vascular plant growth is very limited and largely ephemeral. Extreme abiotic conditions even limit establishment of cyanobacterial soil crusts, with photoautotrophic cyanobacteria largely restricted to the undersides of translucent quartz clasts that buffer environmental extremes. The importance of these ‘hypoliths’ in enhancing SOC pools, and how this may vary with climate and clast physical characteristics, remains unknown. We worked across a rainfall and fog gradient in the central Namib to assess quartz clast size and distribution, factors affecting the probability of hypolithic colonization, and the landscape-level influence of hypoliths on surface SOC pools. Clast colonization increased with clast thickness and with increasing mean annual rainfall. SOC and chlorophyll a (a proxy for cyanobacterial biomass) concentrations were greater under colonized quartz clasts than under non-quartz clasts or in bare soil. Landscape-level SOC, estimated by combining SOC concentration with the distribution and colonization of quartz clasts, was greatest at the site with the highest rainfall and lowest at a mid-gradient site with moderate rainfall and fog. Climate change scenarios that promote quartz colonization have the potential to double SOC pools at the mid-gradient site, although SOC changes would be more muted at other sites. Low vascular plant and biocrust cover in the Namib Desert allows hypolithic communities to play an outsized role in SOC pools; a loss of all hypolithic cyanobacteria would lead to 10–20% declines in surface SOC pools. Future climate change has the potential to shift surface SOC if it alters cyanobacterial colonization of quartz.