The bone marrow stromal microenvironment is damaged in patients with acute leukemia. The aim of this study was to analyze changes associated with the extracellular matrix, mitochondrial function, and vesicular transport in the proteome of multipotent mesenchymal stromal cells (MSCs) in patients at the onset, in remission, before, and 1-3 months after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The study included paired MSCs samples from the bone marrow of 12 patients at the onset and in remission of acute leukemia (4 ALL, 8 AML) and eight patients before and after allo-HSCT (4 ALL, 4 AML). MSCs from eight healthy donors were used as a control. The growth characteristics and the proteome subsets describing extracellular matrix, mitochondria, and vesicular formation were studied. The proteome of the patients' MSCs differed significantly from that of the donor MSCs, both at the onset and in remission. Changes noted in the composition of extracellular matrix proteins may affect cell adhesion and access to growth factors. Significant changes were revealed in proteins affecting mitochondrial function. Vesicular transport proteins also differed between the donor and patient groups. Unexpectedly, no differences were found between the MSCs of donors and patients before and after allo-HSCT.