This study conducts an in-depth economic evaluation of four different types of scrubbers installed on container ships of various sizes. The analysis compares liquefied natural gas (LNG), methanol (MEOH), and very low sulphur fuel oil (VLSFO) with the intermediate fuel oil (IFO) utilised scrubber installation cases. Levelized cost of energy (LCOE) and discounted payback period (DPP) serve as performance indicators under different interest rates (5%, 7%, and 10%) in the scenario-based (minimum, mean, maximum prices) economic calculations. Including the LNG and MEOH scenarios, along with an assessment of the carbon tax effect, represents the innovative contribution of the analysis. Results indicate that the annual fuel consumption of auxiliary engines increases by an average of 257.04 tons with wet scrubber usage. Installation costs of scrubbers vary widely regarding the vessel size and scrubber type. Carbon tax raises annual IFO costs by 35.36% on average. VLSFO, LNG, and MEOH indicate respective annual expenditure increases of 28.37%, 10.78%, and 26.48%. DPPs of open-loop scrubbers are the best among other types for up to 3.85 years. Overall, scrubber installation options outperform alternative fuel utilisation regarding DPP and LCOE metrics, particularly under varying market conditions, emphasising the influence of geopolitical factors on fuel viability.