Elucidating the biological logistics and functional interplay of proteins in their natural context has long been a great challenge in biological research. Chemical modification of proteins allows understanding of their roles and their interactions. Over decades, numerous strategies have been developed to modify target proteins with desired probes in test tubes and even biological systems. Nevertheless, these approaches require the design and synthesis of different probes for different applications, even for the same target protein, which is very time- and labor-consuming. Herein, we developed a general two-step protein functionalization strategy that utilizes ligand-directed chemistry to modify a clickable tag on the intact protein in the first step. Then, the desired functional moiety can be conjugated onto the target protein via a simple bioorthogonal click reaction in the second step, thus achieving probing and activity regulation of the target protein. In this work, carbonic anhydrase (CA) was chosen as our model protein for functionalization. We successfully labeled endogenous CAs with fluorophores to allow cellular imaging. In addition, a photoswitchable ligand was conjugated to CAs such that its activity could be manipulated in a light-responsive manner.