The southeast region of Brazil, in the Atlantic Forest biome, has been impacted for a long time, observing today small agricultural areas inserted in a matrix of pastures and forest fragments, the soils being highly modified due to the different forms of use they were submitted. The objective of this study was to evaluate the organic carbon content in the humic fractions on soil organic matter (SOM), the distribution of aggregates in size classes and the porosity and aggregates density variables by means of computed tomography in secondary forest, pasture and agriculture areas in Pinheiral (RJ). Three areas composed of secondary forests with different succession stages and three managed areas were evaluated: Secondary Forest (SF) Initial Stage (SFIS), Medium Stage (SFMS), Advanced Stage (SFAS), mixed managed pasture (MMP), and perennial and annual agriculture (PA and AA, respectively). Three types of samples were collected in different layers: i) deformed samples to quantify carbon in the SOM humic fractions; ii) clods for quantifying the mass of aggregates and later assessing the distribution by diameter classes; and iii) undisturbed samples collected with the aid of an acrylic cylinder to perform computed tomography (CT). Humic substances and aggregate classes below 2.0 mm were the attributes most influenced by the forms of use and/or vegetation cover. The CT technique proved to be efficient in the measurement of the edaphic attribute’s porosity and density of the aggregates, helping in the characterization and separation of the different environments.