Functionalized nanoparticles (NPs) are complex objects present in a variety of systems ranging from synthetic graftednanoparticles to viruses. The morphology and number of the decorating groups can vary widely between systems. Thus,the modelling of functionalized NPs typically considers simplified spherical objects as a first-order approximation. Atthe nanoscale label, complex hydrodynamic interactions are expected to emerge as the morphological features of theparticles change, and they can be further amplified when the NPs are confined or near walls. Direct estimation of thesevariations can be inferred via diffusion coefficients of the NPs. However, the evaluation of the coefficients requiresan improved representations of the NPs morphology to reproduce important features hidden by simplified sphericalmodels. Here, we characterize the passive transport of free and confined functionalized nanoparticles using the RigidMulti-Blob (RMB) method. The main advantage of RMB is its versatility to approximate the mobility of complex structures at the nanoscale with significant accuracy and reduced computational cost. In particular, we investigate the effectof functional groups distribution, size and morphology over nanoparticle translational and rotational diffusion. We identify that the presence of functional groups significantly affects the rotational diffusion of the nanoparticles, moreover,the morphology of the groups and number induce characteristic mobility reduction compared to non-functionalizednanoparticles. Confined NPs also evidenced important alterations in their diffusivity, with distinctive signatures in theoff-diagonal contributions of the rotational diffusion. These results can be exploited in various applications, includingbiomedical, polymer nanocomposite fabrication, drug delivery, and imaging.