We show that the one- and two-loop β-functions of the closed, bosonic string can be written in a manifestly O(D,D)-covariant form. Based on this result, we prove that1) Poisson-Lie symmetric σ-models are two-loop renormalisable and2) their β-functions are invariant under Poisson-Lie T-duality.Moreover, we identify a distinguished scheme in which Poisson-Lie symmetry is manifest. It simplifies the calculation of two-loop β-functions significantly and thereby provides a powerful new tool to advance into the quantum regime of integrable σ-models and generalised T-dualities. As an illustrating example, we present the two-loop β-functions of the integrable λ- and η-deformation.