A facile and eco-friendly approach using in situ-generated 4-benzenediazonium sulfonate (BDS) was applied to prepare highly functionalized carbon nanotubes (CNTs). The effectiveness of this functionalization was additionally enhanced by a green and short-time ball milling process applied beforehand. The obtained BDS-modified CNTs presented significant activity in glycerol etherification, producing tert-butyl glycerol ethers, which are considered promising fuel additives. Excellent results of ~56% glycerol conversion and ~10% yield of higher-substituted tert-butyl glycerol ethers were obtained within just 1 h of reaction at 120 °C using a low catalyst loading of only 2.5 wt.%. Furthermore, the sulfonated CNTs were reusable over several reaction cycles, with only a minor decrease in activity. Additionally, the sample activity could be restored by a simple regeneration approach. Finally, a clear correlation was found between the content of -SO H groups on the surface of CNTs and the catalytic performances of these materials in glycerol etherification. Improved interaction between functionalized ball-milled CNTs and the reactants was also suggested to positively affect the activity of these catalysts in the tested process.