Increasingly stringent limits for NOx and SO2 emission are forcing the investigation of new reduction methods. This study was conducted to determine the combination of primary measures, i.e., flue gas recirculation (FGR) and excess air effects on sulfur, nitrogen and hydrocarbon emissions, in boiler flue gas. Experimental research was performed using an experimental, small-scale (20 kW) model of an industrial biofuel boiler. During combustion of sunflower seed hulls at different FGR ratios and incomplete combustion regimes, the composition of flue gas (NO, NO2, N2O, HCN, NH3, SO2, SO3, H2S, CO, and CxHy) was compared, allowing an explanation of the determinants of emission concentration changes to be provided. Increasing the flue gas recirculation ratio in the primary air had a positive effect on reducing NOX and CO with certain organic compounds. However, an opposite effect on SO2 was observed. NOX and SO2 concentrations were found to be approximately 500 mg/m3 and 150 mg/m3 under a regular combustion regime. When the FGR ratio of 50% NOX concentration decreased by 110 mg/m3, the SO2 concentration increased by 60 mg/m3. The incomplete combustion regime reduced NOX concentration by 70 mg/m3, whereas SO2 concentration increased by 100 mg/m3. The influence of primary measures presented an unclear relationship to hydrocarbon emissions, with concentrations not exceeding 18 mg/m3.