A system for disinfecting an enclosed area may include a humidity sensor, and a fogging device including a portable housing, an atomizing disinfectant generator carried by the portable housing, at least one output circuit carried by the portable housing, and a processor carried by the portable housing. The processor may be configured to determine a humidity level within the enclosed area based upon the humidity sensor, operate a humidity control device via the at least one output circuit responsive to the determined humidity control level being outside of a starting humidity range, cease operating the humidity control device responsive to the humidity level being within the starting humidity range based upon the humidity sensor, and initiate a treatment cycle during which the atomizing disinfectant generator dispenses atomized disinfectant fluid into the enclosed area.