We present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green's function theory in the GW approximation with the Bethe-Salpeter equation (BSE). This work provides a summary of the underlying theory and discusses the details of its implementation based on Gaussian orbitals, including resolution-of-identity techniques and different approaches to the frequency integration of the self-energy or acceleration by offloading compute-intensive matrix operations using graphics processing units in a hybrid OpenMP/Cuda scheme. A distinctive feature of VOTCA-XTP is the capability to couple the calculation of electronic excitations to a classical polarizable environment on an atomistic level in a coupled quantum- A nd molecular-mechanics (QM/MM) scheme, where a complex morphology can be imported from Molecular Dynamics simulations. The capabilities and limitations of the GW-BSE implementation are illustrated with two examples. First, we study the dependence of optically active electron-hole excitations in a series of diketopyrrolopyrrole-based oligomers on molecular-architecture modifications and the number of repeat units. Second, we use the GW-BSE/MM setup to investigate the effect of polarization on localized and intermolecular charge-transfer excited states in morphologies of low-donor content rubrene-fullerene mixtures. These showcases demonstrate that our implementation currently allows us to treat systems with up to 2500 basis functions on regular shared-memory workstations, providing accurate descriptions of quasiparticle and coupled electron-hole excited states of various characters on an equal footing.