Atomic mapping of nanomaterials, in particular nanoparticles, using atom probe tomography (APT) is of great interest, as their properties strongly depend on shape, size, and composition. However, APT analyses of nanoparticles are extremely challenging, and there is an urgent need for developing robust and universally applicable sample preparation methods. Herein, we explored a method based on pulse electrodeposition to embed Ag nanoparticles in a Ni matrix and prepare APT specimens from the resulting composite film. By systematically varying the duty cycle during pulse electrodeposition, the dispersion and number density of the nanoparticles within the matrix was significantly enhanced as compared to DC electrodeposition. Several Ag nanoparticles were analyzed with APT from such samples. Shape distortions and biased compositions were observed for the Ag nanoparticles after applying a standard data reconstruction protocol. Numerical simulations of the field evaporation process showed that such artifacts were caused by a difference in the evaporation field of Ni and Ag and a local magnification effect. We expect such detrimental effects to be mitigated by a careful selection of the matrix material, matching the evaporation field of the nanoparticles. Furthermore, we anticipate that the method presented herein can be extended to a wider range of nanomaterials.