Functional iron oxide nanoparticles (NP) have been synthesized in a one and a two-step method using a natural functional glycolipid belonging to the family of sophorolipids (SL). These compounds, whose open acidic form is highly suitable for nanoparticle stabilization, are readily obtained by a fermentation process of the yeast Candida bombicola (polymorph Starmerella bombicola) in large amounts. The final carbohydrate coated iron oxide nanoparticles represent interesting potentially biocompatible materials for biomedical applications. According to the synthesis strategy, magnetic properties can eventually be tuned, thus putting in evidence the direct effect of the glycolipid on the final material's structure (maghemite and ferrihydrite have been obtained here). A combination of FT-IR, Dynamic Light Scattering (DLS) and UV-Vis experiments shows that SL complex the nanoparticle surface via their accessible COOH group thus forming stable colloids, whose hydrodynamic diameter mostly varies between 10 nm and 30 nm, both in water and in KCl-containing (0.01 M and 2 M) solutions. The materials can stand multiple filtration steps (up to 10) at different extents, where the largest recorded average aggregate size is 100 nm. In general, materials synthesized at T = 80 °C display better stability and smaller size distribution than those obtained at room temperature.