Bifunctional nanocomposites with superparamagnetic and NIR luminescent properties were synthesized by a layer-by-layer and a modified Stöber method. Fe3O4 nanoparticles as the core were coated with NaYF4:Ln3+ (Ln = Nd, Er, Pr, or Ho) to form the first layer. Then, the second layer was coated with silica to improve the chemical stability and photostability. The X-ray diffraction patterns showed that a cubic spinel structure of Fe3O4 and the coexistence of a cubic and hexagonal structure of NaYF4 were obtained. Energy dispersive X-ray (EDX) spectroscopy analysis confirmed the core/shell structure of Fe3O4@NaYF4:Ln3+. Transmission electron microscopy images revealed that the bifunctional nanocomposites consisted of crystalline Fe3O4@NaYF4:Ln3+ cores and amorphous SiO2 shells, in a spherical shape with a narrow size distribution. Magnetic measurements showed that the obtained bifunctional nanocomposites exhibited superparamagnetic behavior. Emission spectra indicated that the bifunctional nanocomposites possessed a high near-infrared (NIR) luminescent intensity. Moreover, the hexagonal phase NaYF4:Ln3+ showed NIR emission 10 to 15 times stronger than the cubic phase.