This work presents an alternative for adding value to greenhouse crop residues, used for (1) heating and (2) as a CO2 source. Both options are focused on greenhouse agricultural production, but could be applied to other applications. The influence of factors, such as the air/fuel rate and turbulence inside the combustion chamber, is studied. Our results show that for pine pellets, olive pits, tomato-crop residues, and a blend of the latter mixed with almond prunings (75–25%), the thermal losses ranged from 19.5–53.1, 20.5–58.9, 39.9–95%, and 29.4–75.5%, respectively, while the NOX emissions were 30–247, 411–1792, and 361–2333 mg/Nm3, respectively. The above-mentioned blend was identified as the best set-up. The thermal losses were 39.2%, and the CO, NOX, and SO2 concentrations were 11,690, 906, and 1134 mg/Nm3, respectively (the gas concentration values were recalculated for 0% O2). Currently, no other work exists in the literature include a similar analysis performed using a boiler with a comparable thermal output (160.46 kW). The optimal configurations comply with the relevant local legislation. This optimization is important for future emission control strategies relating to using crop residues as a CO2 source. The work also highlights the importance of ensuring a proper boiler set-up for each case considered.