This paper demonstrates secondary aerosol generation potential of biofuel use in the energy sector from the photochemical interactions of precursor gases on a life cycle basis. The paper is divided into two parts—first, employing life cycle analysis (LCA) to evaluate the extent of the problem for a typical biofuel based electricity production system using five baseline scenarios; second, proposing adequate mitigation options to minimise the secondary aerosol generation potential on a life cycle basis. The baseline scenarios cover representative technologies for 2010 utilising energy crop (miscanthus), short rotation coppiced chips and residual/waste wood in different proportions. The proposed mitigation options include three approaches—biomass gasification prior to combustion, delaying the harvest of biomass, and increasing the geographical distance between the biomass plant and the harvest site (by importing the biofuels). Preliminary results indicate that the baseline scenarios (assuming all the biomass is sourced locally) bear significant secondary aerosol formation potential on a life cycle basis from photochemical neutralisation of acidic emissions (hydrogen chloride and sulphur dioxide) with ammonia. Our results suggest that gasification of miscanthus biomass would provide the best option by minimising the acidic emissions from the combustion plant whereas the other two options of delaying the harvest or importing biofuels from elsewhere would only lead to marginal reduction in the life cycle aerosol loadings of the systems.