The capability to embed quantum dots (QDs) at predefined positions in nanophotonic structures is key to the development of complex quantum photonic architectures. Here, we demonstrate that QDs can be deterministically positioned in nanophotonic waveguides by pre-locating QDs relative to a global reference frame using micro-photoluminescence spectroscopy. After nanofabrication, QD-waveguide misalignments of only ($9\pm46$) nm and ($1\pm33$) nm are measured, for QDs embedded in undoped and doped membranes, respectively. A priori knowledge of the QD positions allows us to study the spectral changes introduced by nanofabrication. We record average spectral shifts ranging from 0.1 to 1.1 nm only, indicating that the fabrication-induced shifts can generally be compensated by electrical or thermal tuning of the QDs. Finally, we quantify the effects of the nanofabrication on different charge states of the QDs excitons, showing that this change is constant as a function of QD-to-surface separation, down to distances of only 70 nm. These results show that our approach can deterministically integrate QDs into nanophotonic waveguides whose light-fields contain nanoscale structure and whose spectral response varies at the nanometer level, such as photonic crystal waveguides or cavities.