Gold nanoparticles coated by fluorinated ligands enable formation of new self-assembled materials, molecular recognition and new materials for biomedical applications. •Fluorous gold nanoparticles are promising drug delivery and theranostic platforms.•Fluorophilic interactions are tools for nanoparticles self-assembly.•Fluorophilic interactions enable the formation of patterned mixed monolayers. The development of fluorinated gold nanoparticles is presently arising and increasing attention across several fields of nanotechnology. The synthetic approaches evolved over time from the use of almost perfluorinated alkanethiols and perfluorinated arylthiols to amphiphilic fluorinated thiols capable of ensuring solubility in conventional organic solvents and water. The interest in these systems stems from the unique properties of both nanosized and fluorous compounds. In perspective, the development of our understanding of the fluorophilic interactions at the nanoscale will allow to devise novel strategies for self-assembly, molecular recognition and new materials for biomedical applications. In this paper we present, through selected examples, the potential of fluorous ligands in the synthesis of gold nanoparticles and the relevance of mastering the properties of these systems in the development of new materials.