The capability to embed self-assembled 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 (mu PL) spectroscopy. After nanofabrication, mu PL images reveal misalignments between the central axis of the waveguide and the embedded QD of only (9 +/- 46) nm and (1 +/- 33) nm 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 nm to 1.1 nm, 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 the polarizability, the permanent dipole moment, and the emission frequency at vanishing electric field of different QD charge states, finding that these changes are constant down to QD-surface separations of only 70 nm. Consequently, our approach deterministically integrates QDs into nanophotonic waveguides whose light-fields contain nanoscale structure and whose group index varies at the nanometer level.