In this contribution, motivated by the quest to understand cosmic acceleration, based on the theory of Hořava–Lifshitz and on the branch-cut gravitation, we investigate the effects of non-commutativity of a mini-superspace of variables obeying the Poisson algebra on the structure of the branch-cut scale factor and on the acceleration of the Universe. We follow the guiding lines of a previous approach, which we complement to allow a symmetrical treatment of the Poisson algebraic variables and eliminate ambiguities in the ordering of quantum operators. On this line of investigation, we propose a phase-space transformation that generates a super-Hamiltonian, expressed in terms of new variables, which describes the behavior of a Wheeler–DeWitt wave function of the Universe within a non-commutative algebraic quantum gravity formulation. The formal structure of the super-Hamiltonian allows us to identify one of the new variables with a modified branch-cut quantum scale factor, which incorporates, as a result of the imposed variable transformations, in an underlying way, elements of the non-commutative algebra. Due to its structural character, this algebraic structure allows the identification of the other variable as the dual quantum counterpart of the modified branch-cut scale factor, with both quantities scanning reciprocal spaces. Using the iterative Range–Kutta–Fehlberg numerical analysis for solving differential equations, without resorting to computational approximations, we obtained numerical solutions, with the boundary conditions of the wave function of the Universe based on the Bekenstein criterion, which provides an upper limit for entropy. Our results indicate the acceleration of the early Universe in the context of the non-commutative branch-cut gravity formulation. These results have implications when confronted with information theory; so to accommodate gravitational effects close to the Planck scale, a formulation à la Heisenberg’s Generalized Uncertainty Principle in Quantum Mechanics involving the energy and entropy of the primordial Universe is proposed.