Adherent cells respond to a wide range of substrate cues, including chemistry, topography, hydrophobicity, and surface energy. The cell-substrate interface is therefore an important design parameter in regenerative medicine and tissue engineering applications, where substrate cues are used to influence cell behavior. Thin films comprising 4.5 nm (average diameter) gold nanoparticles coated with a mixture of two alkanethiols can confer hemispherical topography and specific chemistry to bulk substrates. The behavior of murine embryonic stem cells (ESCs) on the thin films can then be compared with their behavior on self-assembled monolayers of the same alkanethiols on vapor-deposited gold, which lack the topographical features. Cells cultured both with and without differentiation inhibitors are characterized by immunofluorescence for Oct4 and qPCR for Fgf5, Foxa2, Nanog, Pou5f1, and Sox2. Nanoscale chemistry and topography are found to influence stem cell differentiation, particularly the early differentiation markers, Fgf5 and Foxa2. Nanoscale topography also affects Oct4 localization, whereas the chemical composition of the substrate does not have an effect. It is demonstrated for the first time that ESCs can sense topographical features established by 4.5 nm particles, and these findings suggest that nanoscale chemistry and topography can act synergistically to influence stem cell differentiation. This study furthers the understanding of the effects of these substrate properties, improving our ability to design materials to control stem cell fate.