Group III-nitride semiconductors have been subject of intensive research, resulting in the maturing of the material system and adoption of III-nitrides in modern optoelectronics and power electronic devices. Defined film polarity is an important aspect of III-nitride epitaxy as the polarity affects the design of electronic devices. Magnetron sputtering is a novel approach for cost-effective epitaxy of III-nitrides nearing the technological maturity needed for device production; therefore, control of film polarity is an important technological milestone. In this study, we show the impact of Al seeding on the AlN/Si interface and resulting changes in crystal quality, film morphology, and polarity of GaN/AlN stacks grown by magnetron sputter epitaxy. X-ray diffraction measurements demonstrate the improvement of the crystal quality of the AlN and subsequently the GaN film by the Al seeding. Nanoscale structural and chemical investigations using scanning transmission electron microscopy reveal the inversion of the AlN film polarity. It is proposed that N-polar growth induced by Al seeding is related to the formation of a polycrystalline oxygen-rich AlN interlayer partially capped by an atomically thin Si-rich layer at the AlN/Si interface. Complementary aqueous KOH etch studies of GaN/AlN stacks demonstrate that purely metal-polar and N-polar layers can be grown on a macroscopic scale by controlling the amount of Al seeding.