Magmatic volatiles can be considered as the surface fingerprint of active volcanic systems, both during periods of quiescent and eruptive volcanic activity. The spatial variability of gas emissions at Earth’s surface is a proxy for structural discontinuities in the subsurface of volcanic systems. We conducted extensive and regular spaced soil gas surveys within the Los Humeros geothermal field to improve the understanding of the structural control on fluid flow. Surveys at different scales were performed with the aim to identify areas of increased gas emissions on reservoir scale, their relation to unknown/knows volcano-tectonic structures on fault scale favoring fluid flow, and determine the origin of gas emissions. Herein, we show results from a carbon dioxide efflux scouting survey, which was performed across the main geothermal production zone together with soil temperature measurements. We identified five areas with increased carbon dioxide emissions, where further sampling was performed with denser sampling grids to understand the fault zone architecture and local variations in gas emissions. We show that a systematic sampling approach on reservoir scale is necessary for the identification and assessment of major permeable fault segments. The combined processing of CO2 efflux and carbon/helium isotopes facilitated the detection of permeable structural segments with a connection to the deep, high-temperature geothermal reservoir, also in areas with low to intermediate carbon dioxide emissions. The results of this study complement existing geophysical datasets and define further promising areas for future exploration activities in the north- and southwestern sector of the production field. The data are presented as one zip folder with 4 data tables (tab delimited text format) according to the measurement variable. The columns are defined in each data file.