Results from the comprehensive fuel testing according to American Society for Testing and Materials International (ASTM) standards of an alkenone-free and decolorized biodiesel produced from the industrially grown marine microalgae Isochrysis sp. are presented. Fatty acid methyl ester (FAME) profiles of the non-decolorized and subsequently decolorized biodiesel fuels were nearly identical, yet the fuel properties were remarkably different. Significant positive impacts on the cetane number, kinematic viscosity, and lubricity were observed, indicating a potential deleterious effect of pigments like chlorophylls and pheophytins on these fuel properties. The decolorization process using montmorillonite K10 gave on average 90% mass recovery, and allowed for an otherwise unobtainable cloud point determination. Oxidative stability of the decolorized Isochrysis biodiesel remained well below the minimum prescribed in biodiesel standards due to elevated content of highly polyunsaturated fatty acids, however other values were in the range of those prescribed in the ASTM standards. Overall, decolorization improved the fuel properties of biodiesel from Isochrysis and may provide a path toward improved biodiesel fuels from other algal species.