Pollutants resulting from domestic combustion would have harmful effects on public health, causing disturbances in the atmosphere chemistry and the climate. In this work, the emissions from the combustion of pellets made of 80% poplar (organically fertilized) and 20% cereal straw (Triticum aestivum) have been analysed. Poplar wood from I-214 and AF-8 clones was obtained from fertilized and non-fertilized plots (CONTROL). Dairy wastewater treatment (MUD) and dehydrated sewage sludge (BIOSOLIDS) were the fertilizers employed. BIOSOLIDS-I214 pellets had lower quality standards, so its combustion was omitted. A flue gas sample was sampled together with the particles emitted. The I-214 MUD sample had the highest emitted CO value (1505 mg/MJ). Regarding HCl emission factors, there was a homogeneity in the results linked with the Cl content present in the raw material. A higher particle emission was associated with pellets with higher ash content. Particles were composed mainly for elemental carbon (26–80 mg/MJ), except I-214 MUD. I-214 pellets had the indicators of incomplete combustion and, therefore, major contaminants emission and major environmental impact. Thus, both the poplar clone and the organic fertilizer influenced the parameters and emissions analysed. Therefore, special attention must be paid to both characteristics.