Wildfires alter aggregate microhabitats that regulate microbial access to carbon in volcanic ash soils, but the persistence of these effects across contrasting climatic windows is poorly understood. We hypothesized that wildfires would reduce cumulative substrate-induced respiration by contracting pore connectivity, with stronger and more persistent effects in native forest microaggregates and plantation macroaggregates. We quantified cumulative substrate-induced CO2 production with the MicroResp whole-soil multiple substrate-induced respiration (MSIR) assay in topsoil (0–5 cm) macroaggregates (2000–250 µm) and microaggregates (250–53 µm) from paired burned and unburned Nothofagus forest and Pinus radiata plantation sites sampled in February 2024 (dry/warm) and August 2024 (wet/cool). Burning lowered total C from 21.8 to 15.2% in the native forest and from 17.5 to 14.3% in the plantation, and reduced meso- and macroporosity. Across campaigns, amino acid cumulative CO2-C in native forest microaggregates decreased from 475 to 181 mg kg−1 in the dry/warm campaign and from 535 to 342 mg kg−1 in the wet/cool campaign, whereas carbohydrate responses in plantation macroaggregates decreased from 372 to 119 mg kg−1 and from 419 to 234 mg kg−1, respectively. Although several contrasts weakened during the wet/cool campaign, fire sensitivity remained concentrated in native-forest microaggregates and plantation macroaggregates. These results support the hypothesis that wildfires reorganize microbial substrate use within aggregates in ways that depend on ecosystem type and aggregate microhabitat structure in volcanic soils.