Commercial scale production of microalgal based biofuels will likely require co-location with a carbon dioxide point source such as coal-fired power plants. Inorganic contaminants innate in coal will ultimately be introduced to the culture system with the potential to impact growth, conversion, and adversely impact the quality of biofuel and other microalgal derived products. Microalgae biomass (Nannochloropsis salina) cultivated in the presence of the inorganic contaminants As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, Sb, Se, Sn, V and Zn was processed into biofuel through one of two different in-situ transesterification methods, 1) acid-catalyzed or 2) supercritical methanol transesterification. The acid catalyzed transesterification resulted in a recovery efficiency increase from 80.5 +/- 6.7% for the control biofuel (uncontaminated biomass conversion) to 88.9 +/- 6.9% for the biofuel containing inorganic contaminants. Supercritical methanol conversion displayed a similar trend corresponding to the recovery efficiency increasing from 98.5 +/- 8.3% for the control biofuel to 100.3 +/- 2.6% for the biofuel containing inorganic contaminants. Inorganic contaminant analysis was performed on all biofuel conversion products and co-products of both transesterification types. Results indicated minimal contamination was found in the biofuel resulting from acid catalyzed transesterification, while substantial contamination was found in the biofuel resulting from supercritical methanol transesterification. Significant amounts of contamination were found in the lipid extracted algae resulting from both types of transesterification. Results show coal flue gas integration with algal production could have negative impacts on yields from standard biofuel conversion processes and limit the end use of bio-based products.