Power quality is an important aspect in data centers and power system operators prefer data centers with high standard power quality. Modern data centers consume large amount of electrical power. As the cooling systems are accounted for 40% of the total power consumption in data centers, energy efficiency in this sector is of high importance. This research investigates if the existing energy efficient cooling strategies can also meet the power quality level defined by the IEEE 519-2014 standard. In this research three automation strategies based on IEC 61499 standard for cooling system in a typical server room are considered and the effects of each one on power quality parameters are investigated via simulation. The investigation has been performed for both; internal power grid of data center and upstream power network that data center is connected to. Power quality parameters which are considered are Total Harmonic Distortion (THD), voltage and current distortions. Results of simulation prove that the automation strategies with highest energy efficiency, also meet the higher power quality standard.