It is well-established that upregulation of drug efflux pumps leads to multi-drug resistance. Less is known about the role of the architecture of the tumor microenvironment in this process: how the location of pump expressing cells influences drug exposure to cancerous as well as non-cancerous cells. Here, we report a 3D in vitro model of spheroids with mixtures of cells expressing high and low levels of ABCG2, quantifying pump activity by the ability to reject the fluorescent dye Hoechst 33342. With respect to the organization of the mixed spheroids, three different architectures were observed: 1) high-expressing ABCG2 cells located in the spheroid core surrounded by low-expressing cells, 2) high-expressing ABCG2 cells intermixed with low-expressing cells and 3) high-expressing ABCG2 cells surrounding a core of low-expressing cells. When high-expressing ABCG2 cells were in the core or intermixed, Hoechst uptake was directly proportional to the percentage of ABCG2 cells. When high-expressing ABCG2 cell formed an outer coating surrounding spheroids, small numbers of ABCG2 cells were disproportionately effective at inhibiting uptake. Specific inhibitors of the ABCG2 transporter eliminated the effect of this coating. Confocal microscopy of spheroids revealed the location of high- and low-expressing cells, and Hoechst fluorescence revealed that the ABCG2-dependant drug concentration in the cancer microenvironment is influenced by pump expression level and distribution among the cells within a tissue. In addition to providing a 3D model for further investigation into multicellular drug resistance, these data show that the location of ABCG2-expressing cells can control drug exposure within the tumor microenvironment.