This study explores the stabilization of non-premixed NH3/CH4 flames using gradient magnetic fields, overcoming challenges like low flame speed and instability inherent in ammonia—a carbon-free fuel and efficient hydrogen carrier. The action of the magnetic field modified the flame flow field, resulting in the suppression of emissions. By applying magnetic fields, the blending ratio of ammonia in the diffusion flame was elevated, resulting in an increase of 69% in the limit concentration to a near-pure level of 0.914. Measurements with Particle Image Velocimetry and schlieren system, alongside computational fluid dynamics, reveal how gradient magnetic fields mitigate flame detachment, lift-off, and blowout by altering flame root stabilization mechanisms. Specifically, gradient magnetic fields reduce localized flow velocity at the flame root and improve mass transfer. This indicates that gradient magnetic fields can significantly enhance the stability of NH3/CH4 flames, suggesting a promising route toward cleaner energy production and environmental sustainability.