Ion sensors work on the principle that the ion current in a combusting mixture is proportional to the electrical conductivity of the mixture. Ion sensors can thus provide direct in-cylinder combustion information to the engine controller in order to optimize engine performance and reduce emissions. Electrical conductivity of the combusting mixture depends on the mixture composition (fuel and equivalence ratio) along with the temperature and pressure. A previously developed equilibrium chemistry model consisting of 20 neutral species and seven charged species was shown to correctly predict the temporal variation of current in a constant-volume, spark-ignited methane/air mixture in a constant volume chamber, for various air/fuel ratios. The current study explores the use of this equilibrium chemistry model for predicting the voltage signatures in a homogeneous charge compression ignition (HCCI) engine fueled with alternative fuels such as propane and acetylene operating at low temperatures and equivalence ratios. Temporal variation of the current signal is compared with experimental data for various equivalence ratios for propane and acetylene. The contribution of various charged species to the current signal is also analyzed. It was seen that the equilibrium chemistry model captures the experimentally observed voltage signal trends correctly for both propane and acetylene for a range of equivalence ratios. The ability of the model to correctly correlate the voltage signal with equivalence ratio for various fuels shows its potential for diagnostics and control of next-generation engines.