Stable isotope C analysis is the most reliable method used for the distinction and understanding of soil carbonates origin. However, in soils with a complex geological setting the carbonate δ13C signature could lead to incorrect interpretations if used alone. Thus coupling this technique to other methods may be necessary. In this work we evaluated advantages and disadvantages of several methods, some of which are well known while others are still unused, to distinguish among carbonates of different origins in a soil developed on “Valle Versa Chaotic Complex”, a marly geological formation in North-western Italy. For a better evaluation of their potentialities the methods were also applied to simpler situations used as a reference for carbonate of pedogenic and lithogenic origins. Thin sections analysis revealed the presence of three kinds of carbonates in the investigated complex soil: one was pedogenic, while two showed clear lithogenic origin. The lithogenic carbonate that showed a low δ13C (about −9‰) was interpreted as freshwater while isotopic signature increased up to −4‰ with the presence of marls, thus no evidence of pedogenic precipitations could be obtained with isotopic analysis. The mean crystallite domain (L104) was highly variable and related to the amounts of co-precipitated impurities in the carbonates. Thus these methods provided important information about the formation environment. These rarely used techniques permitted to distinguish between pedogenic and lithogenic material in simple systems, but did not adequately support the presence of pedogenic carbonates in the complex soil. Surface areas and porosity evaluated by N2 adsorption are particularly influenced by the processes occurring during calcification such as the development of coatings and pore infillings. The comparison between additive models and measured specific surface area, indeed allowed us to observe the effect of pedogenic carbonate on the physical properties, although it did not permit any quantification. These results indicated that, although all the methods were able to distinguish between pedogenic and lithogenic origins in simple systems, only micromorphology and N2 adsorption techniques allowed for the identification of pedogenic carbonate in a more complex soil system.