Several physico-chemical properties of the tumour microenvironment (TME) are dysregulated during tumour progression, such as tissue stiffness, extracellular pH and interstitial fluid flow. Traditional preclinical models, although useful to study biological processes, do not provide sufficient control over these physico-chemical properties, hence limiting the understanding of cause-effect relationships between the TME and cancer cells. Breast cancer stem cells (B-CSCs), a dynamic population within the tumour, are known to affect tumour progression, metastasis and therapeutic resistance. With their emerging importance in disease physiology, it is essential to study the interplay between above-mentioned TME physico-chemical variables and B-CSC marker expression. In this work, 3D in vitro models with controlled physico-chemical properties (hydrogel stiffness and composition, perfusion, pH) were used to mimic normal and tumour breast tissue to study changes in proliferation, morphology and B-CSC population in two separate breast cancer cell lines (MCF-7 and MDA-MB 231). Cells encapsulated in alginate-gelatin hydrogels varying in stiffness (2-10 kPa), density and adhesion ligand (gelatin) were perfused (500 µL/min) for up to 14 days. Physiological (pH 7.4) and tumorigenic (pH 6.5) media were used to mimic changes in extracellular pH within the TME. We found that both cell lines have distinct responses to changes in physico-chemical factors in terms of proliferation, cell aggregates size and morphology. Most importantly, stiff and dense hydrogels (10 kPa) and acidic pH (6.5) play a key role in B-CSCs dynamics, increasing both epithelial (E-CSCs) and mesenchymal cancer stem cell (M-CSCs) marker expression, supporting direct impact of the physico-chemical microenvironment on disease onset and progression. Statement of significanceCurrently no studies evaluate the impact of physico-chemical properties of the tumour microenvironment on breast cancer stem cell (B-CSC) marker expression in a single in vitro model and at the same time. In this study, 3D in vitro models with varying stiffness, extracellular pH and fluid flow are used to recapitulate the breast tumour microenvironment to evaluate for the first time their direct effect on multiple breast cancer phenotypes: cell proliferation, cell aggregate size and shape, and B-CSC markers. Results suggest these models could open new ways of monitoring disease phenotypes, from the early-onset to progression, as well as being used as testing platforms for effective identification of specific phenotypes in the presence of relevant tumour physico-chemical microenvironment.