Abstract Bulgarian coal sample from “Maritza East” lignite deposit, with a significant impact in the total energy supply for the country, is biodesulphurized on laboratory scale. In order to improve the desulphurization effect, sample under study is preliminary chemically treated, i.e. demineralized, depyritized and oxidized. For microbial treatment the microorganism Pseudomonas putida is applied. Maximum total (71.0%), pyritic (90.6%) and organic (49.4%) sulphur desulphurization effects are achieved as a result of combined action of chemical and microbial attacks. The protocol of Maritsa East lignite biotreatment by P. putida bacterial strain persisted on copious washing of the coal. During it, a high volume of dark brown coloured solution has accumulated. After solution acidification by HCl a voluminous precipitate has been formed. The appreciable quantity of this water soluble byproduct provokes us to pay special attention to that material. By applying AP-TPR technique coupled with different detection systems (MS and TD-GC/MS), organic sulphur alterations in chemically and microbiologically desulphurized lignite are assessed. Water soluble byproduct of biodesulphurized coal is also under consideration. It is revealed that as a result of biodesulphurization treatments significant part of S o is transformed in water soluble form, which is highly volatile under AP-TPR experimental condition. The ongoing biodesulphurization mechanism is oxidative with dominance of the C-atom oxidation. Since water soluble byproduct manifests external similarity to humic substances, it is compared to pristine humic acid obtained from the same coal sample. Analysis carried out demonstrates high similarity between both samples.