The standard CISPR 16-1-1 defines the measuring receiver using a black-box approach and sets requirements for its accuracy and spectral properties. Traditionally, such test receivers were developed using a superheterodyne architecture. Recently, time-domain electromagnetic emission measurement systems have been built employing direct sampling instruments, mainly oscilloscopes, and relying on specific signal processing to emulate the performance of compliant instruments. In these cases, the short-time Fourier transform is used for spectral estimation, but the corresponding electromagnetic compatibility standards lack details for its correct use with respect to parameters such as windowing function, overlapping factor, and frequency interpolation. Moreover, it is unclear which combination of spectral estimation parameters is best fit for this purpose. Obtaining reliable, consistent and low uncertainty spectral estimates of electromagnetic emissions measured in time-domain needs appropriate configuration and tuning of the signal processing algorithms. This paper investigates the error in the calculated spectrum for various reference signals: multitone, chirp pulses and rectangular pulses. The analysis is carried out for each CISPR band from A to D, that is, between 9 kHz and 1 GHz. After 489.6 × 10 3 iterations, distributed in 1700 different digital implementations of the CISPR 16-1-1 measuring receiver, the simulations outcomes point to certain sets of parameters that showed satisfactory performance overall, being the Nutall, Kaiser, and Parzen windows with more than 75% of overlapping and using interpolation factor higher than 5, generally suitable. Calibration results are used to experimentally verify that a valid set of parameters is adequate to fulfil CISPR 16-1-1 requirements.INDEX TERMS CISPR-16-1-1, electromagnetic compatibility, measuring receiver, short-time Fourier Transform, standards, time-domain measurements.