A high-speed in-situ laser absorption sensor has been developed for cycle-resolved emissions analysis in the exhaust manifold of production-scale internal combustion engines. An inline sensor module, using optical fiber-coupling of interband and quantum cascade lasers, targets the fundamental rovibrational absorption lines of carbon monoxide and nitric oxide near 5 μm in wavelength. The sensor module was integrated into a commercial EPA-certified natural gas spark-ignition generator operated at 3,300 rpm for measurements of exhaust pulse temperature, CO, and NO concentrations at a rate of 10 kHz. Novel high-temperature optomechanical design enabled in-stream sensor coupling near the exhaust valve with local gas temperatures up to ∼1200 K and valve to sensor gas transit times on the order of milliseconds. Measurement results reveal high degrees of intra-cycle and cycle-to-cycle variations which are otherwise undetectable with standard emission gas analyzers. Sensor response to variations in fuel composition was evaluated by introduction of 1–10% NH3 or H2 into the natural gas fuel system. The effects of fuel blending on exhaust emissions of CO and NO were well-distinguished even at 1% volume fraction, and the sensor captured both intra-cycle and cycle-averaged emissions differences between the three fuel types. Measured concentrations of CO and NO ranged from 0.1–2.8% and 30–3500 ppm with detection limits of 0.07% and 26 ppm, respectively. The exhaust sensor presented here has potential for integration with real-time control systems to enable adaptive optimization of polyfuel internal combustion engines to meet the need for flexible, low-carbon, on-demand energy conversion.