In this paper, we propose a control and optimization framework to reduce network-wide emissions in an urban traffic network. The framework is comprised of two layers. The first layer (optimal green routing) predicts the optimal splitting coefficients for all Origin-Destination (OD) pairs crossing the city center or bypassing. As implementing optimal routing strategies on the field is almost impossible as we do not have direct ontrol over the user's decisions, we choose to balance travel time through gating at the city perimeter so that the usual Dynamic User Equilibrium (DUE) discipline matches the optimal splitting coefficients. The second layer then adjusts inflows at the city gates to the DUE solution based on the instantaneous travel times corresponding to the optimal routing strategy for each OD pair. The accumulation-based Macroscopic Fundamental Diagram (MFD) model of a single reservoir city with seven arterial routes and six bypass alternatives is developed. A Linear programming problem is formulated to determine the optimal splitting coefficients and a Nonlinear Model Predictive Control (NMPC)-based gating control strategy is designed to track the optimal splitting coefficients. The network-wide emission control framework is compared to three other gating strategies aiming to (i) optimize traffic conditions or (ii) minimize emissions, in the inner-city only, and (iii) optimize traffic conditions in the whole network. A comprehensive analysis conducted on all four approaches is presented. We compare the results of the controlled case with respect to the uncontrolled case and with respect to each other. The comparison results show that: (i) the proposed network-wide emission control strategy significantly outperforms the other two simpler control strategies focusing on inner-city only in reducing the total emission, (ii) but also improves the in total time spent and mean speed at the network-level.