This paper presents an integrated energy and emission management strategy, called Integrated Powertrain Control (IPC), for an Euro-VI diesel engine with an electrified waste heat recovery system. This strategy optimizes the CO2–NOx trade-off by minimizing the operational costs associated with fuel consumption, AdBlue dosage, and active particulate filter regeneration, while satisfying the tailpipe emission constraints. For comparison purposes, the proposed control strategy is applied to different powertrain configurations: with and without waste heat recovery (WHR) system and a WHR system equipped with a battery for energy storage. The potential of each studied configuration is evaluated over the World Harmonized Transient Cycle for cold-start and hot-start conditions. In comparison to the existing Euro VI engine without WHR system, it is shown in simulations that the optimal IPC strategy with an electrified WHR system and battery provides an additional 3.5% CO2 emission reduction and 19% particulate matter reduction, while satisfying the NOx emission constraint.