In this work, we investigate the influence that spontaneous emission has on the performance and security of both a qubit and a qutrit quantum key distribution protocols, if these were to be implemented using two- and three-level atoms, respectively. These protocols were developed based on the mechanics of a quantum version of the Monty-Hall game. Our analysis focuses on analyzing the impact that spontaneous emission has on the bit error ratio (BER) and the violation of a Bell-type inequality. In the case of three-level atoms, the three possible configurations (V, Ξ, Λ) are considered. In both protocols, an additional step, consisting on discarding some specific non-valid cases, is found to reduce the BER. Furthermore, our results show that the choice of three-level atom configuration significantly impacts the protocol performance. We are able to determine that the Λ configuration provides a lower BER than the V and Ξ configurations within their respective secure regions.