The economic and environmental performance of microalgal processes has been widely analyzed in recent years. However, few studies propose an integrated process-based approach to evaluate economic and environmental indicators simultaneously. Biodiesel is usually the single product and the effect of environmental benefits of co-products obtained in the process is rarely discussed. In addition, there is wide variation of the results due to inherent variability of some parameters as well as different assumptions in the models and limited knowledge about the processes. In this study, two standardized models were combined to provide an integrated simulation tool allowing the simultaneous estimation of economic and environmental indicators from a unique set of input parameters. First, a harmonized scenario was assessed to validate the joint environmental and techno-economic model. The findings were consistent with previous assessments. In a second stage, a Monte Carlo simulation was applied to evaluate the influence of variable and uncertain parameters in the model output, as well as the correlations between the different outputs. The simulation showed a high probability of achieving favorable environmental performance for the evaluated categories and a minimum selling price ranging from $11 gal− 1 to $106 gal− 1. Greenhouse gas emissions and minimum selling price were found to have the strongest positive linear relationship, whereas eutrophication showed weak correlations with the other indicators (namely greenhouse gas emissions, cumulative energy demand and minimum selling price). Process parameters (especially biomass productivity and lipid content) were the main source of variation, whereas uncertainties linked to the characterization methods and economic parameters had limited effect on the results.