Fluorescent nanodiamonds are versatile tools, which can be employed as perfectly photostable labels as well as for intracellular sensing of a wide array of properties and chemical products due to their fluorescent nitrogen vacancy centres. Since these nanoparticles only probe their environment within a few nanometres, it is essential to deliver them inside the cells and control their intracellular location, which is often achieved by surface functionalization. Another important aspect is the interaction of nanoparticles with the highly complex extra- and intracellular environment. In this paper, we report on the combined functionalization of fluorescent nanodiamond with moieties for the control of surface interactions, and the azide groups, allowing for subsequent covalent attachment of additional functional groups (e.g., antibodies) via click chemistry. Surface functionalized nanodiamonds (fNDs) were delivered into cells using two approaches: incubation with cells and transfection-inspired, polycationic lipid-assisted internalization. The effect of different surface chemistry and different uptake protocols on the cell viability, internalization timing and efficiency, the nanoparticle aggregation inside cells and the intracellular distribution of the fNDs was studied. We showed that both the surface functionalization and the internalization approach had dramatic effects on the fate and behaviour of fluorescent nanodiamonds inside the cells. Our results give an insight into the complex processes underlying the uptake and trafficking of nanodiamonds by the cells, as well as emphasize the need for thorough analysis of the interactions between different functional groups on the nanodiamond surface in cell-based assays. This work lays the foundation for the synthesis of fND derivatives with tailored, multifunctional surfaces.