The present study introduces powder embossing as a novel method to enhance loading of polymeric microcontainers with drug. With current loading approaches, it is not possible to handle pure powder drug in a scalable, homogenous and reproducible manner. In this work, we demonstrate simultaneous loading of 625 microcontainers with powder formulation. This is achieved in a single step by aligning a shadow mask prepared by micro-milling to an array of microcontainers in order to limit drug deposition to the container cavities with diameters of 220μm. A pressure of 8.9MPa is applied by a bonding press and thereby the desired powder is embossed into the container cavities. Powder in the form of pure drug, lipid-based microparticles, and pure polymer was successfully loaded with minimal residues in between the microcontainers and with 100% loaded cavities demonstrating the versatility of the method. The current work is thus contributing to the loading of powder formulations into microscale drug delivery systems such as microcontainers in a facile and reproducible manner.