Even though the role of estrogen receptor alpha (ERα) in the modulation of breast cancer cells' behavior is thoroughly studied, the biological functions of its isoform, ERβ, are less elucidated. The suppression of ERβ in the aggressive ERα-negative MDA-MB-231 breast cancer cells resulted in the inhibition of epithelial to mesenchymal transition (EMT) and major changes in the basic functional properties and expression levels of certain matrix components of breast cancer cells. This arrest in metastatic potential of breast cancer cells suggests the contribution of ERβ in the induction of a more aggressive phenotype in MDA-MB-231 breast cancer cells. The epigenetic alterations are responsible for the ability of the tumor cells to metastasize. Here, we report for the first time that the suppression of ERβ in MDA-MB-231 breast cancer cells leads to significant changes in the expression profiles of specific microRNAs, including miR-10b, miR-200b and miR-145. Growth of MCF-7 and MDA-MB-231 cells in estrogen-free medium has a diverse impact on miRNA expression and the behavior of these cells, suggesting the specific effect of estradiol on the miRNA expression profile depending on the ER status of breast cancer cells. Enhanced miR-10b expression or silencing of miR-145 clearly revealed that these microRNAs can regulate the functional properties, EMT program and the expression of major matrix components known to be implicated in breast cancer aggressiveness. Our data revealed that miR-10b is strongly implicated in the regulation of functional properties, EMT program and Erk1/2 signaling in shERβ MDA-MB-231 cells, thus affecting the extracellular matrix (ECM) composition, including syndecan-1, proteolytic behavior, especially MMP2, MMP7 and MMP9 expression and subsequently the aggressiveness of these cells. Accordingly, the inhibition of miR-145 expression significantly increased the aggressiveness of shERβ MDA-MB-231 cells and induced EMT. Moreover, miR-145 inhibition resulted in important changes in the gene and protein levels of ECM mediators, such as HER2 and several MMPs, whereas it significantly increased the phosphorylated levels of Erk1/2 kinases in these cells, suggesting the crucial role of miR-145 in this signaling pathway. These novel results suggest that the alterations in cell behavior and in ECM composition caused by the suppression of ERβ in MDA-MB-231 cells are closely related to certain epigenetic miRNA-induced alterations. Targeting the ERβ-regulated miR-10b and miR-145 is a promising tool for diagnosis and pharmaceutical targeting in breast cancer.