We exhibit a new pre-Lie algebra in the framework of symplectic groupoids and, in turn, introduce a pre-Lie formalism of Butcher trees for the approximation of Hamilton-Jacobi solutions on any symplectic groupoid $\mathcal{G} \rightrightarrows M.$ The impact of this new algebraic approach is twofold. On the geometric side, it yields algebraic operations to approximate Lagrangian bisections of $\mathcal{G}$ using the Butcher-Connes-Kreimer Hopf algebra and, in turn, aims at a better understanding of the group of Hamiltonian diffeomorphisms of $M.$ On the computational side, we define a new class of Poisson integrators for Hamiltonian dynamics on Poisson manifolds.