Advanced photonic tools may enable researchers and clinicians to visualize, track, control, and manipulate biological processes at the single-cell level in space and time. Biological systems are complex and highly organized on both spatial and temporal levels. If biological entities are to be studied, perturbed, engineered, or healed, key-players in such systems must be visualized and it is required to track, control, and manipulate them precisely and selectively. To achieve this goal, the engineering of nondestructive tools allows to interrogate and manipulate the function of proteins, pathways, and cells for physicians, enabling the design of “smart materials” that can direct and respond to biological processes. Among the potentially exploitable nondestructive tools, light-based actuation is particularly desirable. It enables high spatial and temporal resolution, dosage control, minimal disturbance to biological systems, and deep tissue penetration. Herein, existing approaches toward the engineering of light-activated tools for the interrogation and manipulation of single-cell processes are overviewed, and the types of studies and types of functions that can be controlled by light are listed. Timely applications, such as studies of inflammation and crossing brain barrier systems—via super-resolution imaging and optomechanical manipulation—are two representative examples of emerging applications so far never addressed.