The accurate and rapid prediction of generic nanoscale interactions is a challenging problem with broad applications. Much of biology functions at the nanoscale, and our ability to manipulate materials and engage biological machinery in a purposeful manner requires knowledge of nano-bio interfaces. While several protein-protein interaction models are available, they leverage protein-specific information, limiting their abstraction to other structures. Here, we present NeCLAS, a general, and rapid machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. Two key aspects distinguish NeCLAS: coarsegrained representations, and the use of environmental features to encode the chemical neigh-borhood. We showcase NeCLAS with challenges for protein-protein, protein-nanoparticle and nanoparticle-nanoparticle systems, demonstrating that NeCLAS replicates computationally- and experimentally-observed interactions. NeCLAS outperforms current nanoscale prediction models and it shows cross-domain validity. We anticipate that our framework will contribute to both basic research and rapid prototyping and design of diverse nanostructures in nanobiotechnology.Competing Interest StatementThe authors have declared no competing interest.