Self-driving laboratories (SDLs) are next-generation research and development platforms for closed-loop, autonomous experimentation that combine ideas from artificial intelligence, robotics, and high-performance computing. A critical component of SDLs is the decision-making algorithm used to prioritize experiments to be performed. This SDL “brain” often relies on optimization strategies that are guided by machine learning models, such as Bayesian optimization. However, the diversity of hardware constraints and scientific questions being tackled by SDLs require the availability of a set of flexible algorithms that have yet to be implemented in a single software tool. Here, we report Atlas, an application-agnostic Python library for Bayesian optimization that is specifically tailored to the needs of SDLs. Atlas provides facile access to state-of-the-art, model-based optimization algorithms—including mixed-parameter, multi-objective, constrained, robust, multi-fidelity, meta-learning, and molecular optimization—as an all-in-one tool that is expected to suit the majority of specialized SDL needs. After a brief description of its core capabilities, we demonstrate Atlas’ utility by optimizing the oxidation potential of metal complexes with an autonomous electrochemical experimentation platform. We expect Atlas to expand the breadth of design and discovery problems in the natural sciences that are immediately addressable with SDLs.