Ultrafast spectroscopies can access the dynamics of electrons and nuclei at short timescales, shedding light on nonequilibrium phenomena in materials. However, development of accurate calculations to interpret these experiments has lagged behind as widely adopted simulation schemes are limited to sub-picosecond timescales or employ simplified interactions lacking quantitative accuracy. Here we show a precise approach to obtain the time-dependent populations of nonequilibrium electrons and atomic vibrations (phonons) up to tens of picoseconds, with a femtosecond time resolution. Combining first-principles electron-phonon and phonon-phonon interactions with a parallel numerical scheme to time-step the coupled electron and phonon Boltzmann equations, our method provides unprecedented microscopic insight into scattering mechanisms in excited materials. Focusing on graphene as a case study, we demonstrate calculations of ultrafast electron and phonon dynamics, transient optical absorption, structural snapshots and diffuse X-ray scattering. Our first-principles approach paves the way for quantitative atomistic simulations of ultrafast dynamics in materials.