Biodiesel is typically synthesized from triacylglycerides derived from seed oils (e.g., soybean) and an alcohol (e.g., methanol) with base catalysis, yielding the fatty acid methyl ester, biodiesel. Alternative oil feedstocks (e.g., used cooking oil, rice bran oil, and algae) often have significant quantities of free fatty acids, which greatly complicate the synthesis of biodiesel using the base/methanol method. Here, we have explored a wide range of reaction conditions that optimize biodiesel production from mixed feedstocks containing high free fatty acids. To rapidly survey conditions, a microwave-heated reaction was used to accelerate the reaction and the product was quantified by IH nuclear magnetic resonance NMR spectroscopy. Conditions were determined that allowed for rapid and high yield conversion of oil feedstocks containing significant concentrations of free fatty acids into biodiesel using an acid-catalyzed reaction with longer chain alcohols (such as n-butanol) at a slight molar excess. The conditions were replicated in a traditional heating method, where biodiesel yields greater than 98% were achieved in less than 40 min. Key properties of the resulting butyl-diesel were determined, including cetane, pour point, and viscosity. The information presented should be valuable for the large-scale production of biodiesel from mixed feedstocks that are difficult to use by the base/methanol methods.