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Subterranean rodents can act as ecosystem engineers by shaping the landscape due to soil perturbation and herbivory. At the same time, their burrow density is affected by environmental conditions, vegetation and anthropogenic factors. Disentangling this complex interplay between subterranean rodents and their environment remains challenging. In our study, we analysed the interplay of abiotic conditions, vegetation patterns and human land-use and the burrow density of the giant root-rat (GRR; Tachyoryctes macrocephalus), a subterranean rodent endemic to the Afroalpine ecosystem of the Bale Mountains in south-east Ethiopia. Specifically, we examined the effects of GRR on plant species richness and vegetation cover and vice-versa, and how these reciprocal effects might be modulated by temperature, habitat wetness and grazing. Our results showed that increasing GRR burrow density led to decreased vegetation cover, and that effects of GRR on vegetation cover were slightly stronger than vice-versa. Considering the reciprocal causation models, we found that increasing plant species richness led to increased GRR burrow density, while GRR burrow density decreased as vegetation cover increased. Increases in habitat wetness and livestock grazing intensity also directly led to increased GRR burrow density. Our results stress the importance of subterranean ecosystem engineers on vegetation and highlight the vulnerability of these complex interactions to human activity.