AbstractHydroxyapatite nanoparticles (HAP NPs) are important for medicine, bioengineering, catalysis, and water treatment. However, current understanding of the nanoscale phenomena that confer HAP NPs their many useful properties is limited by a lack of information about the distribution of the atoms within the particles. Atom probe tomography (APT) has the spatial resolution and chemical sensitivity for HAP NP characterization, but difficulties in preparing the required needle‐shaped samples make the design of these experiments challenging. Herein, two techniques are developed to encapsulate HAP NPs and prepare them into APT tips. By sputter‐coating gold or the atomic layer deposition of alumina for encapsulation, partially fluoridated HAP NPs are successfully characterized by voltage‐ or laser‐pulsing APT, respectively. Analyses reveal that significant tradeoffs exist between encapsulant methods/materials for HAP characterization and that selection of a more robust approach will require additional technique development. This work serves as an essential starting point for advancing knowledge about the nanoscale spatiochemistry of HAP NPs.