In the phase diagram of elemental boron, an unknown high-pressure form was identified as γ-orthorhombic boron (γ-B28), provoking studies of the extraordinary properties of its main building blocks, B12 icosahedra and B2 dumbbells. Although two low-pressure phases, α- and β-rhombohedral boron (α-B12 and β-B106), are also composed of icosahedra, the detailed kinetics and mechanisms of the structural transition from α-B12 or β-B106 to γ-B28 remain poorly understood. We report on new metastable boron phases formed during the transition in high-pressure high-temperature conditions that were discovered using the crystal structure search method. The metastable phases are understood to be a three-dimensional buckled defective honeycomb lattice in which boron vacancies lead to a dynamically and mechanically stable structure with triangular motifs. We suggest that the metastable phases act as intermediate states on the transition pathway from α-B12 to γ-B28 owing to their structural flexibility and low enthalpies, in the framework of Ostwald’s step rule.