Pressure difference across the exhaust and intake manifolds (
P) is a crucial variable to control the pumping loss and cylinder charge dilution through the exhaust gas recirculation in a diesel engine. This paper presents a novel architecture for controlling
P and the engine-out NO
x
emissions, which increases the controller tolerance to engine components aging. The architecture has an internal control loop, designed as a two-input two-output controller, to coordinate the exhaust gas recirculation and variable geometry turbine valves. Using feedback from
P and the estimated cylinder oxygen ratio
cyl
, the two-input two-output controller regulates the pumping loss and the engine NO
x
emissions. To reduce high turbo lag and its associated slow air–fuel ratio (
) response, which are inherent features of a
P-based control strategy, the two-input two-output linear quadratic controller is tuned such that
is also regulated, but only during fast transients. An external loop is supplementing the core two-input two-output controller correcting the internal loop set points to reduce the effects of
cyl
estimation errors on NO
x
control and ensure
stays above a minimum value,
min
, critical for smoke emissions. As a feature of the proposed control system, direct feedback from
P increases pumping loss robustness to common degradation in diesel engines, namely, turbine efficiency and diesel particulate filter blockage due to ash deposit, compared to a conventional boost pressure–based controller. Also, it is shown that the input–output coupling structure of the proposed two-input two-output controller and use of the NO
x
feedback mitigate effects of exhaust gas recirculation fouling and associated exhaust gas recirculation valve saturation on increase in NO
x
emission.