We report on the coherent internal-state control of single crystalline nanodiamonds, containing on average 1200 nitrogen-vacancy (NV) centers, embedded in three-dimensional direct-laser-written waveguides. We excite the NV centers by light propagating through the waveguide, and we show that emitted fluorescence can be efficiently coupled to the waveguide modes. We find an average coupling efficiency of 21.6 % into all guided modes. Moreover, we investigate optically-detected magnetic-resonance spectra as well as Rabi oscillations recorded through the waveguide-coupled signal. Our work shows that the system is well suited for magnetometry and remote read-out of spin coherence in a freely configurable waveguide network, overcoming the need for direct optical access of NV centers in nanodiamonds. These waveguide-integrated sensors might open up new applications, like determining magnetic field distributions inside opaque or scattering media, or photosensitive samples, like biological tissue. arXiv:1811.12868v2 [physics.optics]