Two-dimensional (2D) cell cultures have been the primary screening tools to predict drug impacts in vitro for decades. However, owing to the lack of tissue-specific architecture of 2D cultures, secondary screening using three-dimensional (3D) cell culture models is often necessary. A microfluidic approach that facilitates side-by-side 2D and 3D cell culturing in a single microchannel and thus combines the benefits of both set-ups in drug screening; that is, the uniform spatiotemporal distributions of oxygen, nutrients, and metabolic wastes in 2D, and the tissue-like architecture, cell–cell, and cell–extracellular matrix interactions only achieved in 3D. The microfluidic platform is made from an organically modified ceramic material, which is inherently biocompatible and supports cell adhesion (2D culture) and metal adhesion (for integration of impedance electrodes to monitor cell proliferation). To induce 3D spheroid formation on another area, a single-step lithography process is used to fabricate concave microwells, which are made cell-repellant by nanofunctionalization (i.e., plasma porosification and hydrophobic coating). Thanks to the concave shape of the microwells, the spheroids produced on-chip can also be released, with the help of microfluidic flow, for further off-chip characterization after culturing. In this study, the methodology is evaluated for drug cytotoxicity assessment on human hepatocytes.