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Fire is a vital agent of disturbance in African savanna systems, but the relative roles of microhabitat conditions, rainfall and species traits in faunal recolonization need clarification. In order to understand the proximate and ultimate drivers of recolonization after fire, small mammals and microhabitat vegetation were sampled in replicated burned and control sampling areas before and after randomly applied fire in a semi-arid tropical savanna in southern Africa. Vegetation was reduced by fire but had recovered well by the end of the first rainy season. A total of 6851 small-mammal captures were made during 18816 trap nights. Four of the five study species were positively associated with increasing vegetation cover and exhibited strong microhabitat associations. Fire caused a complete turnover of individuals (due to a combination of dispersal and mortality). As predicted using life-history traits, in the first year post-fire, Gerbilliscus leucogaster, Mastomys spp. and Mus indutus were fire positive/fire neutral at a population level, while Steatomys pratensis and Dendromus mesomelas were fire negative/fire neutral. These results are consistent with the hypothesis that each species responds to specific structural elements at the microhabitat level, has a suite of life-history traits that influence their microhabitat associations/response to fire and recolonizes after fire as relevant microhabitat elements recover. The hypothesis that rainfall stimulates microhabitat recovery and thus is a major determinant of the recovery of small-mammal populations after fire was also supported. Given the importance of rainfall, climate change could pose significant conservation challenges in the long term. Continued research on life-history attributes and fire response could result in a useful management tool in the short term.