With a hydrodynamical simulation using a simple galaxy formation model without taking into account feedback, our previous work has shown that dense and massive filaments at high redshift can provide potential wells to trap and compress gas, and hence affect galaxy formation in their resident low-mass haloes. In this paper, we make use of the Auriga simulations, a suite of high-resolution zoom-in hydrodynamical simulations of Milky Way-like galaxies, to study whether the conclusion still holds in the simulations with a sophisticated galaxy formation model. In agreement with the results of our previous work, we find that, compared to their counterparts with similar halo masses in the field, dwarf galaxies residing in filaments tend to have higher baryonic and stellar fractions. At the fixed parent halo mass, the filament dwarfs tend to have slightly higher star formation rates than those of field ones. But overall we do not find a clear difference in galaxy g - r colours between the filament and field populations. We also show that at high redshifts, the gas components in dwarf galaxies tend to have their spins aligned with the filaments in which they reside. Our results support a picture in which massive filaments at high redshift assist gas accretion and enhance star formation in their resident dwarf-sized dark matter haloes.