Large auxiliary engines operated on ocean-going vessels in transit and at berth impact the air quality of populated areas near ports. This paper presents new information on the comparison of emission ranges from three similar engines and the effectiveness of three control technologies: switching to cleaner burning fuels, operating in the low oxides of nitrogen (NOx) mode, and selective catalytic reduction (SCR). In-use measurements of gaseous (NOx, carbon monoxide [CO], carbon dioxide [CO2]) and fine particulate matter (PM2.5; total and speciated) emissions were made on three auxiliary engines on post-PanaMax class container vessels following the International Organization for Standardization-8178-1 protocol. The in-use NOx emissions for the MAN B&W 7L32/40 engine family vary from 15 to 21.1 g/kW-hr for heavy fuel oil and 8.9 to 19.6 g/kW-hr for marine distillate oil. Use of cleaner burning fuels resulted in NOx reductions ranging from 7 to 41% across different engines and a PM2.5 reduction of up to 83%. The NOx reductions are a consequence of fuel nitrogen content and engine operation; the PM2.5 reduction is attributed to the large reductions in the hydrated sulfate and organic carbon (OC) fractions. As expected, operating in the low-NOx mode reduced NOx emissions by approximately 32% and nearly doubled elemental carbon (EC) emissions. However, PM2.5 emission factors were nearly unchanged because the EC emission factor is only approximately 5% of the total PM2.5 mass. SCR reduced the NOx emission factor to less than 2.4 g/kW-hr, but it increased the PM2.5 emissions by a factor of 1.5-3.8. This increase was a direct consequence of the conversion of sulfur dioxide to sulfate emissions on the SCR catalyst. The EC and OC fractions of PM2.5 reduced across the SCR unit.