Traffic congestion and emission are the crucial problems due to its significant impact on the environment, economy, and health of the inhabitants. In this paper, we propose an approach to reduce network-wide emissions in an urban traffic network. The approach is comprised of two layers. The first layer (optimal green routing) which predicts the optimal splitting coefficient for all origin-destination (OD) pairs (only two alternatives are possible for each OD) crossing the city center or bypass it. As implementing optimal routing strategies on the field is almost impossible as we don't have direct control on the users decisions, we choose to balance travel time through gating at the city perimeter in order the usual dynamic user equilibrium (DUE) discipline matches the optimal splitting coefficient derived from the first layer. The second layer then adjusts inflows at the city gates to DUE based on the predictive travel time corresponds to the optimal routing strategy for each OD pair. The accumulation-based macroscopic fundamental diagram (MFD) model of a single reservoir city with seven atrial routes and six bypass alternatives is developed. Linear programming (LP) problem is formulated to determine the optimal splitting coefficients (first layer) and the nonlinear model predictive control (NMPC)-based gating control strategy is designed to track the optimal splitting coefficients (second layer). Combination of two layers indirectly track the network-wide emission levels by manipulating the traffic flows into the reservoir. The network wide emission control approach is compared with another usual gating strategy (perimeter control) aiming to optimize traffic conditions in the inner-city only. The comprehensive analysis conducted on proposed approach is presented. We compare the results of controlled case with respect to the uncontrolled case and with respect to each other. The comparison results show: (i) the proposed network-wide emission control approach outperforms congestion control approach in reducing the total emission, (ii) significant improvements in total time spent, mean speed, and emission are obtained when considering both the inner-city and the bypass traffic with the network-wide strategy and (iii) improvements come at the cost of increased complexity (need to solve two optimization problems).