► We study Macroscopic Fundamental Diagrams in networks with traffic signals. ► We simulate these networks using an efficient cellular automata model. ► MFDs depend strongly on the specific control strategy of the traffic signals. ► MFDs do exist for biased demand, but their shapes depend on the bias. ► Hysteresis can be clockwise or anticlockwise, depending on heterogeneity. Using a stochastic cellular automaton model for urban traffic flow, we study and compare Macroscopic Fundamental Diagrams (MFDs) of arterial road networks governed by different types of adaptive traffic signal systems, under various boundary conditions. In particular, we simulate realistic signal systems that include signal linking and adaptive cycle times, and compare their performance against a highly adaptive system of self-organizing traffic signals which is designed to uniformly distribute the network density. We find that for networks with time-independent boundary conditions, well-defined stationary MFDs are observed, whose shape depends on the particular signal system used, and also on the level of heterogeneity in the system. We find that the spatial heterogeneity of both density and flow provide important indicators of network performance. We also study networks with time-dependent boundary conditions, containing morning and afternoon peaks. In this case, intricate hysteresis loops are observed in the MFDs which are strongly correlated with the density heterogeneity. Our results show that the MFD of the self-organizing traffic signals lies above the MFD for the realistic systems, suggesting that by adaptively homogenizing the network density, overall better performance and higher capacity can be achieved.