Quantum dots (QDs) are semiconductor nanocrystals, which present unique photophysical properties, enabling their application as new fluorescent platforms for biomedical sciences. Colloidal QDs are end-capped with organic or inorganic compounds, not only to prevent their agglomeration but also to provide reaction sites for the attachment of targeting (bio)molecules, nanoparticles or other interfaces, for specific biological purposes. The (bio)conjugation can involve non-covalent or covalent interactions, which can be accomplished through different strategies. The final assembly needs to maintain its chemical and optical stability and biochemical functionality. Although a relative good comprehension of the experimental procedures has been established, the bioconjugation process is still a challenge. The present manuscript aims to review the main (bio)conjugation strategies successfully applied to QDs, describing the steps necessary to prepare stable targeting fluorescent nanoplatforms, as well as some usual methods used to evaluate and optimize this process.