Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non‐targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non‐targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high‐throughput single‐cell profiling data. Single‐cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.