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A comparison of methods for measuring time-of-flight (TOF) variations of ultrasonic waves travelling through food materials is presented. Six commonly used methods for the TOF determination were taken into account, four in the time domain and two in the frequency domain. First, methods were briefly described and then tested using simulated ultrasonic waves. Factors such as signal-to-noise ratio (SNR), attenuation and delay between signals are taken into consideration, whereas the root mean-squared error (RMSE) and execution time are used as parameters for comparison. Of the six methods, the one operating on the basis of phase shift proved to be the most robust and provided excellent levels of resolution and optimum performance across a wide range of SNR values. Experiments were subsequently conducted in a real process, which corroborated the results obtained during the theoretical study. The ability to accurately measure TOF variations of ultrasonic waves makes it possible to detect more precisely velocity variations, which is the most commonly used parameter to determine and acoustic monitor physicochemical changes and properties of food materials.