Primordial magnetic fields (PMFs) could explain the large-scale magnetic fields present in the universe. Inflation and phase transitions in the early universe could give rise to such fields with unique characteristics. We investigate the magnetohydrodynamic evolution of these magnetogenesis scenarios with cosmological simulations. We evolve inflation-generated magnetic fields either as (i) uniform (homogeneous) or as (ii) scale-invariant stochastic fields, and phase-transition-generated ones either as (iii) helical or as (iv) nonhelical fields from the radiation-dominated epoch. We find that the final distribution of magnetic fields in the simulated cosmic web shows a dependence on the initial strength and the topology of the seed field. Thus, the observed field configuration retains information on the initial conditions at the moment of the field generation. If detected, PMF observations would open a new window for indirect probes of the early universe. The differences between the competing models are revealed on the scale of galaxy clusters, bridges, as well as filaments and voids. The distinctive spectral evolution of different seed fields produces imprints on the correlation length today. We discuss how the differences between rotation measures from highly ionized regions can potentially be probed with forthcoming surveys.