With the spread of low-cost computing and access to automated software, it is becoming increasingly common for users to perform parameter set optimization prior to running molecular mechanics simulations. However, this optimization is typically used to supplement existing transferable force fields and is limited to the charge and torsional parameters, for which well-established protocols for fitting to QM data exist. On the other hand, QM de-rived force fields allow the user to obtain all (or most) of the force field parameters directly from ab initio calculations, but for these methods scaling to large molecules is problematic and there is no clear route to the simulation of, for example, biomolecular complexes. In this paper, we present the QUBEKit software for automated derivation of virtually all force field parameters required to model the dynamics of small organic molecules. QUBEKit is a python interface that brings together methods for charge and Lennard-Jones parameter derivation from atoms-in-molecule analysis of the QM electron density, and a method for deriving bond and angle force constants directly from the QM Hessian matrix. We also include a method for off-center virtual site derivation along with an automated implementation of a standard one-dimensional torsion fitting scheme.