The behavior of three-dimensional (3D) semimetals under strong magnetic fields is a topic of recurring interest in condensed matter physics. Recently, the advent of Weyl and Dirac semimetals has brought about an interesting platform for potentially uncovering phases of matter that combine nontrivial band topology and interactions. While electronic instabilities of such semimetals at strong magnetic fields have been explored theoretically and experimentally, the role of electron-phonon interactions therein has been largely neglected. In this paper, we study the interplay of electron-electron and electron-phonon interactions in a minimal two-node model of Weyl semimetal. Using a Kadanoff-Wilson renormalization group approach, we analyze lattice (Peierls) instabilities emerging from chiral and nonchiral Landau levels as a function of the magnetic field. We consider both the adiabatic and the nonadiabatic phonon regimes, in the presence or in the absence of improper symmetries that relate Weyl nodes of opposite chirality. We find that (i) the Cooper channel, often neglected in recent studies, can prevent purely electronic instabilities while enabling lattice instabilities that are not Bardeen-Cooper-Schrieffer-like; (ii) breaking the improper symmetry that relates the two Weyl nodes suppresses the Cooper channel, thereby increasing the critical temperature for the lattice instability; (iii) in the adiabatic phonon regime, lattice instabilities can preempt purely electronic instabilities; (iv) pseudoscalar phonons are more prone to undergo a Peierls instability than scalar phonons. In short, our study emphasizes the importance of taking electron-phonon interactions into account for a complete understanding of interacting phases of matter in Dirac and Weyl semimetals at high magnetic fields.