A system for managing power in a transport refrigeration unit, TRU, installed on a trailer, comprising: TRU power supply components including a TRU battery; TRU power demand components including a TRU controller and one or more of a TRU compressor, a TRU evaporator, a TRU condenser, TRU cargo lights, TRU heaters and a TRU controller interactive display; wherein the TRU controller is configured to: execute a system-level energy manager function; adaptively select energy flow parameters based on one or more mission specific parameters and TRU power health; execute a predictive analytics module for collecting mission specific parameters and predicting TRU cooling power demands; execute an online optimization module for generating a power source schedule for the TRU based on the predicted TRU cooling power demands; and operate the TRU according to the generated power source schedule; wherein the one or more mission specific parameters include one or more of actual and forecast in-route weather and traffic conditions, driver preferences defining a minimum duration of time between connecting to an electrical grid charging station, and in-route proximity to an electrical grid charging station; and wherein the TRU power health includes an observed and a pan-mission anticipated state of TRU power supply components and power demand components. TRU power supply components including a TRU battery; TRU power demand components including a TRU controller and one or more of a TRU compressor, a TRU evaporator, a TRU condenser, TRU cargo lights, TRU heaters and a TRU controller interactive display; wherein the TRU controller is configured to: execute a system-level energy manager function; adaptively select energy flow parameters based on one or more mission specific parameters and TRU power health; execute a predictive analytics module for collecting mission specific parameters and predicting TRU cooling power demands; execute an online optimization module for generating a power source schedule for the TRU based on the predicted TRU cooling power demands; and operate the TRU according to the generated power source schedule; wherein the one or more mission specific parameters include one or more of actual and forecast in-route weather and traffic conditions, driver preferences defining a minimum duration of time between connecting to an electrical grid charging station, and in-route proximity to an electrical grid charging station; and wherein the TRU power health includes an observed and a pan-mission anticipated state of TRU power supply components and power demand components. execute a system-level energy manager function; adaptively select energy flow parameters based on one or more mission specific parameters and TRU power health; execute a predictive analytics module for collecting mission specific parameters and predicting TRU cooling power demands; execute an online optimization module for generating a power source schedule for the TRU based on the predicted TRU cooling power demands; and operate the TRU according to the generated power source schedule; wherein the one or more mission specific parameters include one or more of actual and forecast in-route weather and traffic conditions, driver preferences defining a minimum duration of time between connecting to an electrical grid charging station, and in-route proximity to an electrical grid charging station; and wherein the TRU power health includes an observed and a pan-mission anticipated state of TRU power supply components and power demand components.