Integrated nanophotonic circuits made from wide-bandgap semiconductors offer exciting prospects for advanced sensing applications and broadband optical data processing. Among the available substrates, diamond is particularly appealing due to its long-term stability, biocompatibility and chemical inertness. Because of strong field confinement in diamond waveguides, near-field effects can be efficiently harnessed to realize building blocks for biofunctional circuits in a scalable fashion. Here, we report on the parallel and site-specific functionalization of diamond nanophotonic devices as a promising route towards waferscale bio-photonic systems. We show that arbitrary geometric features can be surface modified using dip-pen nanolithography with a minimum linewidth of 100 nm. We simultaneously functionalize several microring and microdisc resonators with different dies and high precision, allowing us to route fluorescent emission with photonic waveguides to arbitrary locations on chip. Our approach holds promise for hybrid optical systems and nanoscale bioactive devices for robust biomedical and environmental high-throughput sensing applications.2 Photonic components made from diamond have emerged as a promising platform for applications in quantum optics [1][2][3][4], non-linear optics [5,6] and optomechanics [7,8].Because of its remarkable material properties such as broadband optical transparency, high mechanical stability and hardness, high thermal conductivity, and good chemical stability, diamond is used for a wealth of applications in research and industrial environments. In particular the combination of appealing optical properties and biocompatibility make diamond an attractive platform for biophotonic applications [9][10][11]. Nowadays high quality diamond thin films are available on large-scale substrates by relying chemical vapor deposition (CVD) which allows for using waferscale processing techniques to realize functional devices. In this way homogeneous large scale diamond thin films can be achieved (see Supplementary Fig. S2). Using nanofabrication routines developed originally for the electronics industry CVD diamond thin films can be structured into subwavelength photonic devices, which allow for propagating light over centimeter distances, the realization of high quality optical resonators and on-chip interferometers [8,12]. This way the powerful toolbox available to integrated optics can be efficiently utilized to realize a sensitive readout platform for biological signals.In order to employ integrated photonic devices for biosensing suitable links to desired analytes have to be established. Several techniques are commonly employed to functionalize pre-structured photonic substrates, including spincoating with suitable coatings introduced in the liquid phase [13,14] and exposure to reactive agents in the gas phase [15]. While such techniques are suitable to functionalize many photonic components uniformly, it is ultimately necessary to only target specific locations on chip. Deposition of ...