Gas-phase emission samples of carbonyl compounds (CCs) were collected from two modern wood combustion appliances. Multiple repetitions were conducted on masonry heater operated with three logwood species (birch, beech, and spruce) and for a pellet boiler operated by softwood pellet with normal combustion and unoptimized combustion (in which the secondary combustion air flow rate was decreased). The sampling of CCs was performed from diluted exhaust using 2,4-dinitrophenylhydrazine (DNPH) cartridges. The CCs-hydrazone derivatives were analyzed by a gas chromatography–selective ion monitoring–mass spectrometry (GC-SIM-MS) method. Twelve (12) CCs were quantified in the masonry heater emissions and 8 in the pellet boiler emissions. The total carbonyl emission factors (EFs) for logwood were determined to be as follows: birch, 113 ± 18 mg kg–1; beech, 178 ± 31 mg kg–1; spruce, 171 ± 19 mg kg–1; and, for softwood pellet with normal combustion, 6 ± 0.9 mg kg–1 and for softwood pellet with unoptimized combustion, 6.5 ± 1 mg kg–1. In masonry heater operation, birch exhibits the lowest emission factors, compared to other wood types. No significant differences were noticed between the emission of normal and unoptimized combustion for the pellet boiler operation. The emission profile examination showed that formaldehyde and acetaldehyde were the predominated carbonyls in the emission, regardless of the wood type. Time-resolved results obtained via single-photon ionization time-of-flight mass spectrometry (SPI-TOFMS) depict that, in masonry heater emissions, most carbonyls are produced as a new batch of wood is introduced.