Purpose The aims of this paper were to review tools and methods for qualitative and quantitative evaluation of soil organic matter (SOM) coming from diverse egzogenic sources for effective soil management, and to introduce a new approach to predict dynamics of SOM transformations, especially humification, as a key process in the formation of humic substances (HSs). Materials and methods A review of existing literature is presented on tools and methods for qualitative and quantitative assessment of organic matter in soil originating from various sources for reasonable soil management, attempting to provide a better understanding of the advances in organic matter transformations and new research directions for modeling. Diverse tools and methods for qualitative and quantitative evaluation of organic matter in soil coming from diverse sources have been adopted so far to express transformation processes. Results and discussion For the qualitative analysis of SOM and humic acids (HAs), the analytical techniques are applied, e.g., HPSEC, NMR, and ESI-FTICRMS. The quantitative analysis is done through the following parameters: humification index (HI), humification degree (HD), and humification rate (HR). These analyses indicated that because of lack of reliable data from sufficiently long-term experiments, mathematical modeling may be applied as a numerical tool for quantitative estimation and prediction of humification of SOM. The effective soil management should include soil properties as well as different functions: food production, nutrient and water cycling, storage, filtrating, buffering, biological habitat, gene pool, source of raw materials, climate regulations, heritage, platform for man-made structure. The soil utility value should be evaluated through the SOM qualitative and quantitative analysis of organic carbon and total nitrogen. Knowledge about dynamics of SOM transformations is essential, particularly in the context of stability and efficiency of different sources of organic matter applied into soil. A qualitative understanding of SOM dynamics transformations along with modeling for quantitative assessment of HS formation should be used to develop sustainable soil management. The modeling may be considered as a tool for predicting SOM humification dynamics and consequently the formation of HSs from the diverse sources. The existing archival data from a long-term experiment may be used to build and calibrate the reliable mathematical model of SOM humification. Conclusions Managing of SOM remains a sound basis for maintaining soil in a good condition for optimizing productivity. The development of land management strategies to optimize both the increase of soil organic carbon levels and the recycling of nutrients from SOM needs to be a priority. This should include policy makers and other users as well.