Although it is relatively easy to set-up, the monitoring of soil temperature in sub-fumarolic areas is quite rarely used to monitor the evolution of hydrothermal systems. Indeed, measurements are highly sensitive to environmental conditions, in particular daily and seasonal variations of atmospheric temperatures and rainfalls, which can be only partially filtered by the established statistical analysis. In this paper, we develop two innovative processing methods, both based on the computation of the heat flux in the soil. The upward heat flux method (UHF), designed for dry environments, consists in computing both the conductive and convective components of the heat flux between two thermocouples placed vertically. In the cases of wet environments, the excess of total heat method (ETH) allows the integration of rain gauges data in order to correct the heat balance from the superficial cooling effect of the precipitations. The performances of both processing techniques are faced to established methods (temperature gradient and coefficient of determination) on soil temperature time series from two test volcanoes. At La Fossa di Vulcano (Italy), the UHF method undoubtedly detects three thermal crises between 2009 and 2012, enabling to quantify not only the intensity but also the precise timing of the heat flux increase with respect to corresponding geochemical and seismic crises. At La Soufrière de Guadeloupe (French Lesser Antilles), despite large rainfalls dramatically influencing the thermal behavior of the soil, a constant geothermal heat flux is retrieved by the ETH method, confirming the absence of fumarolic crisis during the observation period (February–August 2010). Being quantitative, robust, and usable in almost any context of sub-fumarolic zones, our two heat flux-based methods increase the potential of soil temperature for the monitoring, but also the general interpretation of fumarolic crises together with geochemical and seismological observations. A spreadsheet allowing direct computation of UHF and ETH is provided as supplemental material.