Optical imaging technologies and cell targeting have played a major role in detecting and treating diseases such as cancer. Bioharmonophores are optical imaging nanoprobes composed of biodegradable polymer-encapsulated, self-assembling triphenylalanine peptides. They produce a strong second harmonic generation (SHG) signal, a non-linear optical process in which two photons directed at a non-centrosymmetric medium combine to form a new photon with twice the energy. Bioharmonophores demonstrate superior optical properties compared to fluorescent probes and, unlike previously developed inorganic SHG nanoprobes, are both biocompatible and biodegradable. Here, we present a protocol providing five detailed procedures that describe (1) synthesis of bioharmonophores; (2) embedding and imaging of the synthesized SHG nanoprobes in polyacrylamide gel; (3) functionalization of bioharmonophores with thiol-containing polyethyleneglycol; (4) subsequent click chemistry to target cancer cells; and (5) imaging of functionalized bioharmonophores endocytosed by cancer cells using two-photon microscopy. Bioharmonophores hold great potential as clinical contrast agents due to their optical features and could be used in the future as an innovative approach to cancer treatment using targeted high-resolution optical imaging. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Synthesis of bioharmonophores Basic Protocol 2: Imaging of bioharmonophores in polyacrylamide gel Basic Protocol 3: Functionalization of bioharmonophores with thiol-PEG Basic Protocol 4: Functionalization of thiol-PEGylated bioharmonophores with peptides Basic Protocol 5: Targeting of cancer cells with functionalized bioharmonophores.