The coating of porous scaffolds with nanoparticles is crucial in many applications, for example to generate scaffolds for catalysis or to make scaffolds bioactive. A standard and well-established method for coating surfaces with charged nanoparticles is electrophoresis, but when used on porous scaffolds, this method often leads to a blockage of the pores so that only the outermost layers of the scaffolds are coated. In this study, the electrophoretic coating process is monitored in situ and the kinetics of nanoparticle deposition are investigated. This concept can be extended to design a periodic electrophoretic deposition (PEPD) strategy, thus avoiding the typical blockage of surface pores. In the present work we demonstrate successful and homogeneous electrophoretic deposition of hydroxyapatite nanoparticles (HAn, diameter ≤200 nm) on a fibrous graphitic 3D structure (ultralightweight aerographite) using the PEPD strategy. The microfilaments of the resulting scaffold are covered with HAn both internally and on the surface. Furthermore, protein adsorption assays and cell proliferation assays were carried out and revealed that the HAn-decorated aerographite scaffolds are biocompatible. The HAn decoration of the scaffolds also significantly increases the alkaline phosphatase activity of osteoblast cells, showing that the scaffolds are able to promote their osteoblastic activity.