Methods of controlling transport climate control systems are provided to reduce the impact of their operation on the sleep of an occupant, who can be in a nearby sleeping space. Methods include obtaining occupant sleep status data, determining one or more operational parameters of the transport climate control system based on the occupant sleep status data, and operating the transport climate control system according to the one or more operational parameters to control when at least one of a motor, a compressor, a generator, or one or more fans are in operation during an occupant sleep state. The methods can be implemented by a controller of a transport climate control system or a control module for such a system.