The formation and evolution of F-induced nanobubbles in Si was investigated. Si samples were preamorphized, implanted with F, and partially regrown by solid phase epitaxy (SPE). It is shown that nanobubbles are formed already in the amorphous side of partially regrown samples and are then incorporated in crystalline Si during SPE. The bubbles are interpreted as the result of the diffusion and coalescence of F atoms and dangling bonds already in the amorphous matrix. During high temperature annealing after SPE, F outdiffuses; correspondingly, the bubbles partially dissolve and transform from spherical- to cylinder-shaped bubbles.