Superparamagnetic Iron Oxide Nanoparticles (SPIONs) have attracted a great deal of research attention due to their enormous possibilities of utilisation in different bioapplications such as magnetic particle imaging, drug delivery, hyperthermia or magnetic bio-detection. The purpose of this review is to critically analyze the methods for synthesis of SPIONs reported at the literature taking into account their suitability in molecular recognition applications by means of their conjugation to biomolecules. In this work, we have summarized the main synthesis routes, and controlled agglomeration methods for enhancement of sensitivity at molecular recognition events. This includes conventional chemical precipitation methods, thermal decomposition, microemulsions, or microfluidic synthesis, and the main strategies for the preparation of nanocomposites or SPIONs nanoclusters, such as polymer or silica cross-linking reactions, entrapment in nanovesicles or flower-like structures through the appropriate use of different metals to get synergetic properties for the total nanoarquitecture. Since most of the actual applications in biomedicine require their conjugation to biomolecules, an analysis of the Strengths, Weaknesses, Opportunities and Threats of these methods was carried out for the first time, with a view to highlight the best routes for a given application at biomolecular recognition.