Magnetic skyrmions, topological vortex-like spin textures, garner significant interest due to their unique properties and potential applications in nanotechnology. While they typically form a hexagonal crystal with distinct internal magnetisation textures known as Bloch- or Néel-type, recent theories suggest the possibility for direct transitions between skyrmion crystals of different lattice structures and internal textures. To date however, experimental evidence for these potentially useful phenomena have remained scarce. Here, we discover the polar tetragonal magnet EuNiGe₃ to host two hybrid skyrmion phases, each with distinct internal textures characterised by anisotropic combinations of Bloch- and Néel-type windings. Variation of the magnetic field drives a direct transition between the two phases, with the modification of the hybrid texture concomitant with a hexagonal-to-square skyrmion crystal transformation. We explain these observations with a theory that includes the key ingredients of momentum-resolved Ruderman–Kittel–Kasuya–Yosida and Dzyaloshinskii-Moriya interactions that compete at the observed low symmetry magnetic skyrmion crystal wavevectors. Our findings underscore the potential of polar magnets with rich interaction schemes as promising for discovering new topological magnetic phases.