Understanding phase transitions of ultrathin metal silicides is crucial for the development of nanoscale silicon devices. Here, the phase transition of ultrathin (3.6 nm) Ni silicides on Si(100) substrates is investigated using an in situ synthesis and characterization approach, supplemented with ex situ transmission electron microscopy and nano-beam electron diffraction. First, an ultrathin epitaxial layer and ordered structures at the interface are observed upon room-temperature deposition. At 290 °C, this structure is followed by formation of an orthorhombic δ-Ni2Si phase exhibiting long-range order and extending to the whole film thickness. An unprecedented direct transition from this δ-Ni2Si phase to the final NiSi2−x phase is observed at 290 °C, skipping the intermediate monosilicide phase. Additionally, the NiSi2−x phase is found epitaxial on the substrate. This transition process substantially differs from observations for thicker films. Furthermore, considering previous studies, the long-range ordered orthorhombic δ-Ni2Si phase is suggested to occur regardless of the initial Ni thickness. The thickness of this ordered δ-Ni2Si layer is, however, limited due to the competition of different orientations of the δ-Ni2Si crystal. Whether the formed δ-Ni2Si layer consumes all deposited nickel is expected to determine whether the monosilicide phase appears before the transition to the final NiSi2−x phase.