We demonstrate the use of sequential catalytic growth to encapsulate iron, nickel-iron, and iron-cobalt phosphide catalyst nanoparticles periodically along the entire lengths of carbon nanotubes. Investigations by local electron spectroscopies and electron diffraction reveal the compositions and crystal structures of the encapsulated particles. Significantly, high spatial resolution magnetic characterization using magnetic force microscopy and off-axis electron holography demonstrates that encapsulated iron-cobalt phosphide nanoparticles are ferromagnetic at room temperature, in accordance with the properties of bulk metal phosphides of the same structure and composition.