Bone marrow (BM) involvement in B-cell non-Hodgkin lymphoma (B-NHL) is associated with poor prognosis, as the BM microenvironment provides a protective niche that promotes therapeutic resistance. We developed a simplified, automated and high-throughput 3D BM co-culture model that faithfully reproduces key tumour-stroma interactions. In our system, BM stromal cells (BMSCs) decreased lymphoma cell sensitivity to Phosphatidylinositol 3-kinase (PI3K) and BTK inhibitors. Moreover, we show that our 3D platform enables the mechanistic studies of microenvironment-mediated drug resistance and has the potential to be developed into a tool for personalized therapeutic strategies for B-NHL.