The decarbonization process of the automotive industry and the road transport sector has raised the interest on the development of cleaner fuels. A proper characterization of their properties and behavior under different operating conditions is mandatory to achieve an effective implementation in commercial engines. With this objective, the current work presents a comparison of two injectors from the Engine Combustion Network (ECN), namely Spray A and Spray D injectors, in terms of spray characteristics and combustion behavior for different fuels: diesel, dodecane, Hydrotreated Vegetable Oil (HVO), and two types of oxymethylene ethers (OME1 and OME x). The aim is to analyze how differences in nozzle geometry affect the behavior of different types of fuels. The experiments were carried out in a High Temperature and High Pressure test rig and operating conditions were chosen following ECN guidelines. Visualization techniques such as high speed schlieren imaging, OH* chemiluminescence and diffused back illumination were implemented to analyze the differences in liquid length, vapor penetration, auto ignition, flame lift-off length, and soot formation for both nozzles. In general, results showed the same trend for all the fuels tested: longer liquid length and faster vapor penetration for Spray D, as well as higher ignition delay and longer lift-off length. However, it was found that these parameters were less sensitive to the nozzle diameter for the oxygenated fuels tested. Furthermore, a different trend was observed for OME1, in terms of ignition behavior, in comparison to the other fuels. In terms of soot production, the Spray D nozzle increases its formation with the non-oxygenated fuels. In contrast, no soot was observed with the oxygenated ones under any operating conditions.