Herein, we demonstrate the control of magnetotactic bacteria through the application of magnetic field gradients with real-time visualization. We accomplish this control by integrating a pair of macroscale Helmholtz coils and lithographically fabricated nanoscale islands composed of permalloy (Ni₈₀Fe₂₀). This system enabled us to guide and steer amphitrichous Magnetospirillum magneticum strain AMB-1 to specific location via magnetic islands. The geometries of the islands allowed us to have control over the specific magnetic field gradients on the bacteria. We estimate that magnetotactic bacteria located less than 1 μm from the edge of a diamond shaped island experience a maximum force of approximately 34 pN, which engages the bacteria without trapping them. Our system could be useful for a variety of applications including magnetic fabrication, self-assembly, and probing the sensing apparatus of magnetotactic bacteria.