Abstract Understanding arctic ecosystem function is key to understanding future global carbon (C) and nutrient cycling processes. However, small mammal herbivores can have effects on ecosystems as structure builders and these effects have been underrepresented in the understanding of arctic systems. We examined the impact of small mammal structures (hay piles, runways, latrines) on soils and plants in three arctic tundra regions near Utqiaġvik, Toolik Lake, and Nome, Alaska. Our aims were to (1) examine how vole and lemming structures influence plant and soil nutrient pools and microbial processes, (2) determine if structure effects were similar across tundra system types, and (3) understand how changes in the abundance and cover of these structures during different phases of small mammal multi‐annual population cycles might influence biogeochemical cycling. In general, small mammal structures increased nitrogen (N) availability in soils, although effects varied by study region. Across study regions, hay piles were relatively uncommon (lowest % cover) but increased multiple soil N and P pools, C‐ and N‐acquiring enzyme activities, and leaf phosphorus (P) concentrations, with the specific nutrient variables and size of the effects varying by study region. Latrines had the second highest cover and influenced multiple C, N and P pools, but their effects were mainly observed within a single region. Lastly, runways had the highest % cover of all activity types but increased the fewest number of soil nutrient variables. We conclude that by influencing soil nutrient availability and biogeochemical cycling, small mammal structures can influence bottom‐up regulation of ecosystem function, particularly during the high phase of the small mammal population cycle. Future changes in these population cycles might alter the role of small mammals in the Arctic and have lasting effects on system processes. Read the free Plain Language Summary for this article on the Journal blog