The homogeneous charge compression ignition (HCCI) engine can be run on a large range of fuels if the appropriate operating conditions are chosen. This can improve the efficiency of biofuel production from low-value biomass by suppressing the need for the transformation process to obtain products that are compatible with spark ignition or compression ignition engines. A simple biochemical process that includes acidogenic fermentation and produces a mixture of various esters can take advantage of this flexibility. However, the behavior of this mixture under HCCI conditions needs to be characterized. It can also have a great impact on the HCCI operating limits and its successful implementation. Using an HCCI engine, we investigated how the operating limits are modified by the combustion characteristics of three of these esters: ethyl acetate, ethyl propionate, and ethyl butanoate. This paper reports the experimental results for each of these products and for ethanol taken as the reference fuel. It also analyzes their effects on the ignition timing and the combustion rate. For the selected operating conditions, stable HCCI operations on a large range of equivalence ratios were obtained for every fuel The difference in specific heats of the air/fuel mixtures and in the ignition kinetics both contributed to the ignition characteristics. Ethanol ignites earlier, which leads to a low upper limit, whereas the late ignition of ethyl acetate shifts the operating zone upward due to smoothed high loads but unstable low loads. As a consequence, these low-grade products can be used in an HCCI engine. Fuel blends of these products may take advantage of the different combustion characteristics to extend the HCCI zone. Still, the range of this extension is difficult to estimate and the research of the optimal fuel blend composition will, therefore, remain the focus of future work.