Climatic warming is predicted to affect high-latitude habitats, such as boreal peatlands, at a larger magnitude than the global average. The controls on the breakdown of organic matter in peatlands are complex; it’s unclear how climatic warming will affect the stability of the large carbon pool that’s currently stored in peatlands. To investigate this, we collected soil cores from three boreal habitats along a hydrological transect (Bog, Intermediate, and Upland Forest) in Finland, and incubated ex-situ for 140 days. Each soil horizon was incubated in three temperatures (0°C, 4°C, 20°C). Here, we found the Intermediate site had the largest CO2 production considering the entirety of the soil column (per gram dry weight). Statistical analysis found that sample C content was the most indicative independent variable to predict sample CO2 production. Each soil horizon displayed a different magnitude of response to the temperature incubations (Q10s ranged from 0.60-2.33), and through microbial relative abundance analysis we found that the microbial community structure had significant differences between both habitat and depth of sample origin. Coupling these methods, and the fine scale of the both vertical (soil column horizons) and horizontal (along a hydrological gradient through distinct habitats) transects gives us a novel perspective on the controls of microbial respiration rates. Our results stress that large scale modeling efforts of carbon dynamics should prioritize both soil carbon quantity and quality.