The aim of this study was to obtain hierarchical scaffolds combining 3D printing and two electrofluidodynamic methods. The multi-layered scaffold is composed by 3D printed struts, electrospun fibers obtained from poly(ε-caprolactone) (PCL) and electrosprayed spheres produced from hydrophobically modified chitosan, namely chitosan grafted with linoleic acid (CHLA). Since CHLA has been used for the first time in the electrospraying (EDS) process, the formation of spheres needed an optimization process. The EDS process was strongly affected by the solvent mixture composition, concentration of acid used for CHLA dissolution and solution flow rate. By using the optimized electrospraying conditions, uniformly distributed spheres have been obtained, decorating struts and nanofibers. Preliminary biological tests with mouse preosteoblasts (MC3T3-E1) were performed to investigate the effect of the hierarchical scaffold on cell seeding efficacy. Results showed that the hierarchical structure enhances cell seeding efficacy, respect to the 3D printed struts alone, preventing that the cells passed through the struts during the seeding. Moreover, the addition of the electrosprayed nanoparticles does not affect the cell seeding efficiency. The versatility of the proposed structure, with the added value of CHLA nanoparticles decoration could be suitable for several applications in tissue engineering, mainly related to drug delivery systems.