Changes in soil fertility during pedogenesis affect the quantity and quality of resources entering the belowground subsystem. Climate governs pedogenesis, yet how climate modulates responses of soil food webs to soil ageing remains unexplored because of the paucity of appropriate model systems. We characterised soil food webs along each of four retrogressive soil chronosequences situated across a strong regional climate gradient to show that belowground communities are predominantly shaped by changes in fertility rather than climate. Basal consumers showed hump-shaped responses to soil ageing, which were propagated to higher-order consumers. There was a shift in dominance from bacterial to fungal energy channels with increasing soil age, while the root energy channel was most important in intermediate-aged soils. Our study highlights the overarching importance of soil fertility in regulating soil food webs, and indicates that belowground food webs will respond more strongly to shifts in soil resources than climate change.