A method for providing environmental condition control of a multi-zone transport refrigeration system (MTRS) within three or more zones of a refrigerated transport unit, the refrigerated transport unit including a first zone, a second zone and a third zone, and the MTRS including a host unit configured to provide environmental control within the first zone, a first remote unit configured to provide environmental control within the second zone and a second remote unit configured to provide environmental control within the third zone, the method characterized by comprising: a MTRS controller determining whether either of a second zone environmental condition difference and a third zone environmental condition difference is greater than a first threshold, wherein the second zone environmental condition difference is a difference between a second zone measured environmental condition and a second zone desired set point environmental condition and wherein the third zone environmental condition difference is a difference between a third zone measured environmental condition and a third zone desired set point environmental condition; and the MTRS controller, when the second zone environmental condition difference is determined to be greater than the first threshold: operating the first remote unit; determining whether the third zone environmental condition difference is greater than a second threshold; operating the second remote unit when the third zone environmental condition difference is determined to be greater than the second threshold, the second threshold being a lower temperature value than the first threshold such that the MTRS controller directs the refrigerant flow through the first remote unit and the second remote unit at the same time; and preventing operation of the second remote unit when the third zone environmental condition difference is determined to be less than or equal to the second threshold. a MTRS controller determining whether either of a second zone environmental condition difference and a third zone environmental condition difference is greater than a first threshold, wherein the second zone environmental condition difference is a difference between a second zone measured environmental condition and a second zone desired set point environmental condition and wherein the third zone environmental condition difference is a difference between a third zone measured environmental condition and a third zone desired set point environmental condition; and the MTRS controller, when the second zone environmental condition difference is determined to be greater than the first threshold: operating the first remote unit; determining whether the third zone environmental condition difference is greater than a second threshold; operating the second remote unit when the third zone environmental condition difference is determined to be greater than the second threshold, the second threshold being a lower temperature value than the first threshold such that the MTRS controller directs the refrigerant flow through the first remote unit and the second remote unit at the same time; and preventing operation of the second remote unit when the third zone environmental condition difference is determined to be less than or equal to the second threshold. operating the first remote unit; determining whether the third zone environmental condition difference is greater than a second threshold; operating the second remote unit when the third zone environmental condition difference is determined to be greater than the second threshold, the second threshold being a lower temperature value than the first threshold such that the MTRS controller directs the refrigerant flow through the first remote unit and the second remote unit at the same time; and preventing operation of the second remote unit when the third zone environmental condition difference is determined to be less than or equal to the second threshold.