Uncertain systems are those wherein some variability is observed, meaning that different observations of the system will produce different measurements. Studying such systems demands the use of statistical methods over multiple measurements, which allows overcoming the uncertainty, based on the premise that a single measurement is not representative of the system’s behavior. In such cases, the current multifractal detrended fluctuation analysis (MFDFA) method cannot offer confident conclusions. This work presents multi-signal MFDFA (MS-MFDFA), a novel methodology for accurately characterizing uncertain systems using the MFDFA algorithm, which enables overcoming the uncertainty of the system by simultaneously considering a large set of signals. As a case study, we consider the problem of characterizing software (Sw) consumption. The difficulty of the problem mainly comes from the complexity of the interactions between Sw and hardware (Hw), as well as from the high uncertainty level of the consumption measurements, which are affected by concurrent Sw services, the Hw, and external factors such as ambient temperature. We apply MS-MFDFA to generate a signature of the Sw consumption profile, regardless of the execution time, the consumption levels, and uncertainty. Multiple consumption signals (or time series) are built from different Sw runs, obtaining a high frequency sampling of the instant input current for each of them while running the Sw. A benchmark of eight Sw programs for analysis is also proposed. Moreover, a fully functional application to automatically perform MS-MFDFA analysis has been made freely available. The results showed that the proposed methodology is a suitable approximation for the multifractal analysis of a large number of time series obtained from uncertain systems. Moreover, analysis of the multifractal properties showed that this approach was able to differentiate between the eight Sw programs studied, showing differences in the temporal scaling range where multifractal behavior is found.