At low temperatures $T$ where $\nicefrac{1}{T}=\beta\gg1$ the na"ive implementation of determinant quantum Monte Carlo (DQMC) methods suffers from loss of precision and numerical instabilities when evaluating the fermion determinant. In double precision the simulations of systems with a band width $\Delta$ deteriorate around $\beta \Delta \approx 70$. This instability propagates into the calculation of observables that rely on the evaluation of the inverse of the fermion matrix, or the Green’s function. For DQMC methods that rely on the Hamiltonian Monte Carlo (HMC) algorithm, an additional complication comes from evaluating the force terms required for integrating Hamilton’s equations of motion, since here loss of precision and numerical instabilities are also prevalent. We show how to address all these issues using various choices of matrix decompositions, allowing us to simulate at $\beta \gtrsim 100$ or $\beta \Delta \gtrsim 600$, which corresponds to room temperature for graphene structures. Furthermore, our implementation has numerical costs that scale similarly to the na"ive implementation, namely as $𝒪(N_x^3{N}_t)$, where $N_x$ ($N_t$) is the number of spatial (temporal) sites.