Structural anisotropy is ubiquitous in nature and governs orientation-dependent properties and functions1,2. Recreating biomimetic anisotropy in hydrogels—water-rich soft materials widely used in biomedicine—has proven challenging3. Here we report a phenomenon termed shear-extensional in situ particle-to-fibre transformation (SHIFT) and demonstrate the SHIFT printing of highly aligned hydrogel microfibres (5–30 μm in diameter). In SHIFT, particle-embedded hydrogel is extruded in a controlled manner, in which the discrete particles and surrounding matrix experience opposite phase transitions, concurrently transforming particles into well-aligned subvoxel microfibres. SHIFT establishes a methodology for creating anisotropy from droplets, which is dominated by extensional flow of sol–gel two-phase systems. It constitutes a versatile upstream manufacturing approach that can be readily adapted into three-dimensional printing and microfibre spinning scenarios in a highly accessible manner. The pronounced structural anisotropy enables the formation of exceptionally long myotubes in vitro and accelerates regeneration in volumetric muscle loss. By implementing an in situ subvoxel manufacturing process within flow, SHIFT expands the ability to process soft materials.