The study analysed how carbon dynamics were influenced by the transition from coal or natural gas to forest biomass on a number of district heat and combined heat and power plants in Denmark. For 10 plants, we calculated the cumulative net carbon emissions over time (t) from the fuel transition (CCE(t)) and carbon payback time (CPT), a measure of the time it takes for a fuel transition to biomass to reduce the amount of carbon emitted to the atmosphere relative to a continuation of using fossil fuels. Subsequently, we derived the relative cumulative net carbon emissions (RCCE(t)), as a measure of the carbon emission savings/costs induced by the fuel transition. Finally, we performed sensitivity analyses of key parameters, with special focus on emissions from indirect/market mediated effects. For fuel transitions from coal to biomass, CPT ranged from 0 to 13 years indicating that carbon emission benefits were achieved at the latest after 13 years. Relative cumulative net carbon emissions 30 years after the fuel transition (RCCE(30)) ranged from 0.29 to 0.85 corresponding to emission savings of 15–71% relative to continued use of coal. For fuel transitions from natural gas to biomass, CPT ranged from 9 to 34 years and RCCE(30) from 0.81 to 1.03. Sensitivity analyses showed that the use of truly residual biomass (harvest residues or industrial residues with no alternative use), biomass harvest from productive forests and short transport distances are instrumental in achieving a short carbon payback time and large emission savings. The quantification of indirect or market mediated GHG emissions is controversial and uncertain. We analysed additional carbon emissions related to indirect land use change (iLUC), indirect wood use change (iWUC) and indirect fuel use change (iFUC). Including iLUC added 1–4 years, iWUC added 1–3 years and iFUC added 1 year to the mean CPT.