Stirling units are a viable option for micro-cogeneration applications, but they operate often with multiple daily startups and shutdowns due to the variability of load profiles. This work focused on the experimental and numerical study of a small-size commercial Stirling unit when subjected to cycling operations. First, experimental data about energy flows and emissions were collected during on−off operations. Second, these data were utilized to tune an in-house code for the economic optimization of cogeneration plant scheduling. Lastly, the tuned code was applied to a case study of a residential flat in Northern Italy during a typical winter day to investigate the optimal scheduling of the Stirling unit equipped with a thermal storage tank of diverse sizes. Experimentally, the Stirling unit showed an integrated electric efficiency of 8.9% (8.0%) and thermal efficiency of 91.0% (82.2%), referred to as the fuel lower and, between parenthesis, higher heating value during the on−off cycling test, while emissions showed peaks in NOx and CO up to 100 ppm but shorter than a minute. Numerically, predictions indicated that considering the on−off effects, the optimized operating strategy led to a great reduction of daily startups, with a number lower than 10 per day due to an optimal thermal storage size of 4 kWh. Ultimately, the primary energy saving was 12% and the daily operational cost was 2.9 €/day.