A method is presented for combining atomic force microscopy (AFM) force mode and fluorescence microscopy in order to (a) mechanically stimulate immune cells while recording the subsequent activation under the form of calcium pulses, and (b) observe the mechanical response of a cell upon photoactivation of a small G protein, namely Rac. Using commercial set-ups and a robust signal coupling the fluorescence excitation light and the cantilever bending, the applied force and activation signals were very easily synchronized. This approach allows to control the entire mechanical history of a single cell up to its activation and response down to a few hundreds of milliseconds, and can be extended with very minimal adaptations to other cellular systems where mechanotransduction is studied, using either purely mechanical stimuli or via a surface bound specific ligand. •A signal coupling AFM and fluorescence microscopy was characterized for soft cantilevers.•It can be used as an intrinsic timer to synchronize images and forces.•Mechanical stimulation of single immune cells while recording calcium fluxes was detailed.•Light-induced mechanical modifications of lymphocytes using a PA-Rac protein were demonstrated.•The precautions and limitations of use of this effect were presented.