Modeling efforts to understand the financial implications of microalgal biofuels often assume a static basis for microalgae biomass composition and cost, which has constrained cultivation and downstream conversion process design and limited in-depth understanding of their interdependencies. For this work, a dynamic biological cultivation model was integrated with thermo-chemical/biological unit process models for downstream biorefineries to increase modeling fidelity, to provide mechanistic links among unit operations, and to quantify minimum product selling prices of biofuels via techno-economic analysis. Variability in design, cultivation, and conversion parameters were characterized through Monte Carlo simulation, and sensitivity analyses were conducted to identify key cost and fuel yield drivers. Cultivating biomass to achieve the minimum biomass selling price or to achieve maximum lipid content were shown to lead to suboptimal fuel production costs. Depending on biomass composition, both hydrothermal liquefaction and a biochemical fractionation process (combined algal processing) were shown to have advantageous minimum product selling prices, which supports continued investment in multiple conversion pathways. Ultimately, this work demonstrates a clear need to leverage integrated modeling platforms to advance microalgae biofuel systems as a whole, and specific recommendations are made for the prioritization of research and development pathways to achieve economical biofuel production from microalgae.