Cement production is among the largest contributors to industrial air pollution, emitting ~3 Mt NOx/year. The industry-standard mitigation approach, selective non-catalytic reduction (SNCR), exhibits low NH3 utilization efficiency, resulting in operational inefficiencies and increased reagent costs. Here, we develop a data-driven framework for emission control using large-scale operational data from four cement plants worldwide. Benchmarking nine machine learning architectures, we observe that prediction error varies ~3-5x across plants due to variation in data richness. Incorporating short-term process history nearly triples NOx prediction accuracy, revealing that NOx formation carries substantial process memory, a timescale dependence that is absent in CO and CO2. Further, we develop models that forecast NOx overshoots as early as nine minutes, providing a buffer for operational adjustments. The developed framework controls NOx formation at the source, reducing NH3 consumption in downstream SNCR. Surrogate model projections estimate a ~34-64% reduction in NOx while preserving clinker quality, corresponding to a reduction of ~290 t NOx/year and ~58,000 USD/year in NH3 savings. This work establishes a generalizable framework for data-driven emission control, offering a pathway toward low-emission operation without structural modifications or additional hardware, with potential applicability to other hard-to-abate industries such as steel, glass, and lime.