Updated project metadata. Breast cancer remains one of the leading causes of death in women, being the chemotherapeutic agent doxorubicin (Dox) among the most widely standard chemotherapy options for its treatment. However, its effective use has been severely limited owing to its well-documented cardiotoxic side effect that can lead to heart failure in a subset of patients. We have previously shown that a specific population of mesenchymal stem cells (MSCs) present immunomodulatory and regenerative properties, mainly granted by its secretome (CM), whose potential was improved when produced under 3D conditions. In cancer, the role of MSCs is still contradictory, with literature reporting both cancer promoting and suppressive effects. Therefore, we aimed at determining the effect of concomitant exposure of Dox with CM from 3D (CM3D) and 2D (CM2D) MSC cultures in breast cancer cells (MDA-MB-231) and in non-tumour breast epithelial cells (MCF10A) and differentiated AC16 cardiomyocytes. As such, the whole secretome was obtained by collecting and concentrating the culture media conditioned by MSCs in 2D (CM2D) and 3D (CM3D). A Ge-LC-MS/MS proteomic analysis revealed that CM3D effects may be linked to MSC cytoprotection and tumour development, namely through regulation of cell proliferation (CAPN1, CST1, LAMC2, RANBP3), migration (CCN3, MMP-8, PDCD5), invasion (TIMP-1/2), oxidative stress (AIFM1, CD9, GSR) and inflammation (ANXA5, CDH13, GDF-15). Overall, MSC-derived CM3D decreased Dox-induced cytotoxic effects on non-tumour breast cells and cardiomyocytes, without compromising Dox chemotherapeutic nature, highlighting the potential use of CM3D as an adjuvant in chemotherapy to reduce off-target side effects.