Surface-functionalized nanomaterials are of interest as theranostic agents that detect disease and track biological processes using hyperpolarized magnetic resonance imaging (MRI). Candidate materials are sparse however, requiring spinful nuclei with long spin-lattice relaxation (T1) and spin-dephasing times (T2), together with a reservoir of electrons to impart hyperpolarization. Here, we demonstrate the versatility of the nanodiamond material system for hyperpolarized 13C MRI, making use of its intrinsic paramagnetic defect centers, hours-long nuclear T1 times, and T2 times suitable for spatially resolving millimeter-scale structures. Combining these properties, we enable a new imaging modality, unique to nanoparticles, that exploits the phase-contrast between spins encoded with a hyperpolarization that is aligned, or anti-aligned with the external magnetic field. The use of phase-encoded hyperpolarization allows nanodiamonds to be tagged and distinguished in an MRI based on their spin-orientation alone, and could permit the action of specific bio-functionalized complexes to be directly compared and imaged.