We report the cultivation of Chlorella sorokiniana str. SLA-04 in media containing trace amounts of Ca and Mg. The differences in productivities of biomass, lipids and carbohydrates were assessed relative to cultures grown in standard media (BG-11) that contain approximately 8 � higher concentration of Ca and 30 � higher concentration of Mg. Culture performance in N-limited standard media was also investigated. In addition to growth and accumulation of storage products (lipid and carbohydrate), we measured the utilization of N, Ca and Mg and monitored changes in cell size and photosynthetic activity. Our results showed that limitation of Ca or Mg did not inhibit cell replication and culture growth. On the contrary, Ca-limited (Ca<
sup>
L<
/sup>
) cultures had ~30% higher biomass productivity relative to the control with excessive nutrients possibly due to improvement in cell wall flexibility and cell division. We also observed that Ca<
sup>
L<
/sup>
and Mg-limited (Mg<
sup>
L<
/sup>
) cultures had nearly 3-fold higher lipid concentration (measured as fatty acid methyl ester) and 50% higher carbohydrate concentration than the nutrient excess control cultures. Simultaneous culture growth and lipid accumulation in Ca<
sup>
L<
/sup>
and Mg<
sup>
L<
/sup>
cultures suggest that de novo synthesis was the primary mechanism for lipid accumulation in Ca/Mg-limited media. Overall, our study demonstrates that micronutrient optimization, in addition to optimization of macronutrients, could significantly improve microalgal biorefinery yields.