Conversion, drainage, and cultivation of tropical peatlands can change soil conditions, shifting the C balance of these systems, which is important for the global C cycle. We examined the effect of soil organic matter (SOM) quality and nutrients on CO2 production from peat decomposition using laboratory incubations of Indonesian peat soils from undrained forest in Kalimantan and drained oil palm plantations in Kalimantan and Sumatra. We found that oil palm soils had higher C/N and lower SOM quality than forest soils. Higher substrate quality and nutrient availability, particularly lower ratios of aromatic/aliphatic carbon and C/N, rather than total SOM or carbon, explained the higher rate of CO2 production by forest soils (10.80 ± 0.23 µg CO2–C g C h-1) compared to oil palm soils (5.34 ± 0.26 µg CO2–C g C h-1) from Kalimantan. These factors also explained lower rates in Sumatran oil palm (3.90 ± 0.25 µg CO2–C g C h-1). We amended peat with nitrogen (N), phosphorus (P), and glucose to further investigate observed substrate and nutrient constraints across the range of observed peat quality. Available N limited CO2 production, in unamended and amended soils. P addition raised CO2 production when substrate quality was high and initial P state was low. Glucose addition raised CO2 production in the presence of added N and P. Our results suggest that decline in SOM quality and nutrients associated with conversion may decrease substrate-driven rates of CO2 production from peat decomposition over time.