This study considers a fabrication of magnetoactive scaffolds based on a copolymer of vinylidene fluoride and trifluoroethylene (P(VDF-TrFE)) and 5, 10, and 15 wt.% of magnetite (Fe3O4) nanoparticles modified with citric (CA) and oleic (OA) acids by solution electrospinning. The synthesized Fe3O4-CA and Fe3O4-OA nanoparticles are similar in particle size and phase composition, but differ in zeta potential values and magnetic properties. Pure P(VDF-TrFE) scaffolds as well as composites with Fe3O4-CA and Fe3O4-OA nanoparticles demonstrate beads-free 1 μm fibers. According to scanning electron (SEM) and transmission electron (TEM) microscopy, fabricated P(VDF-TrFE) scaffolds filled with CA-modified Fe3O4 nanoparticles have a more homogeneous distribution of magnetic filler due to both the high stabilization ability of CA molecules and the affinity of Fe3O4-CA nanoparticles to the solvent used and P(VDF-TrFE) functional groups. The phase composition of pure and composite scaffolds includes a predominant piezoelectric β-phase, and a γ-phase, to a lesser extent. When adding Fe3O4-CA and Fe3O4-OA nanoparticles, there was no significant decrease in the degree of crystallinity of the P(VDF-TrFE), which, on the contrary, increased up to 76% in the case of composite scaffolds loaded with 15 wt.% of the magnetic fillers. Magnetic properties, mainly saturation magnetization (Ms), are in a good agreement with the content of Fe3O4 nanoparticles and show, among the known magnetoactive PVDF or P(VDF-TrFE) scaffolds, the highest Ms value, equal to 10.0 emu/g in the case of P(VDF-TrFE) composite with 15 wt.% of Fe3O4-CA nanoparticles.