Two-band superconductors exhibit a distinct phase characterized by two correlation lengths, one smaller and the other larger than the magnetic field penetration length. This regime was coined type-1.5 superconductivity, with several unconventional properties, such as vortex clustering. However, a fully microscopic solution for vortex clusters has remained challenging due to computational complexities beyond quasiclassical models. This work presents numerical solutions obtained in a fully self-consistent two-band Bogoliubov-de Gennes model. We show the presence of discrepant correlation lengths leading to vortex clustering in two-band superconductors.