The Serra das Éguas Complex, in Brumado, state of Bahia, located in the northeastern region of Brazil, is a geological structure comprising volcanochemical, siliciclastic and carbonate units that contain layers and lenses of magnesite, important as a refractory in steel, cement, glass and copper and other applications. Considering the importance of such sort of deposit, this work aims to (i) study the physical properties of magnesite deposits via direct measurements of radiometric spectrometry and magnetic susceptibility associated with chemical analysis of the available borehole core samples; (ii) analyse the magnetic and radiometric data acquired by the combined airborne survey over the area with known magnesite deposits; (iii) estimate the magnetic response of the magnesite deposits and surrounding rock formations via 2D forward and 3D inverse magnetic modelling; (iv) evaluate and, if necessary, reconsider the stratigraphic sequences of the identified geological units of the Complex using the results of the 2D and 3D magnetic modelling. Through forward/inverse models, we noted an expressive magnetic signature likely related to the iron formations and metamafic and meta‐ultramafic rocks. The radiometric data analysis on the drill cores showed that the reddish magnesite has a well‐defined U/Th signature. Furthermore, the results show that the carbonate unit, which contains the magnesite deposits, has the lowest amplitude of magnetization values, and both signatures might be helpful for their identification. Additionally, the magnetic models show that the carbonate unit lies in the upper part of the stratigraphic sequence of the Serra das Éguas Complex. This conclusion drives us to propose a new stratigraphy sequence, where the volcanochemical unit that includes the iron formations lies at the bottom of this stratigraphic sequence.