The combination of materials that possess different properties (such as, for instance, fluorescence and magnetism) into one single object of nanoscale size represents an attractive challenge for biotechnology, especially for their potential relevance in biomedical applications. We report here the preparation of novel bifunctional conjugates based on the linkage of inorganic nanoparticles to organic oligothiophene fluorophores (OTFs). In comparison to the organic dyes commonly used in bioimaging and more similarly to colloidal quantum dots, OTFs have broad optical absorption spectra, and therefore OTF fluorophores emitting at different colors can be excited with a single excitation source, allowing for easier multiplexing analysis. In this work we show the preparation of OTF-nanoparticle conjugates based on gold and iron oxide nanoparticles and their characterization using different techniques such as gel electrophoresis, photoluminescence spectroscopy, dynamic light scattering, and so on. In addition, by performing an in vitro study on human tumor cells we show that OTF-nanoparticle conjugates emitting at different colors can be used for multiplexing detection. Also, in the case of iron oxide-OTF conjugates, once uptaken by the cells, we show that they preserve both their fluorescent and their magnetic properties.