An HVAC controller, such as a thermostat, may be configured to allow a user to set and/or select schedule time period in which one or more indoor quality units (e.g. humidification, dehumidification, ventilation, etc.) will or will not operate, and/or will operated but using different settings. In some cases, the schedule time periods available for selection may correspond to the time periods of a programmable temperature schedule of the HVAC controller, but this is not required. In some instances, the HVAC controller may allow a user to select which indoor air quality units will or will not operate, and/or what settings the indoor air quality units will operate, during a user's vacation.