A technique facilitates automatic commissioning operations on pumping systems, e.g. electric submersible pumping systems. The automatic commissioning technique employs closed-loop monitoring and control processes which may include monitoring of pump shaft direction and speed measurements. In many applications, the technique reduces the time and manual effort otherwise involved in commissioning pumping systems in well completions. Embodiments also may be employed in automated decision-making related to commissioning and in determining operational settings based on sensed environmental and/or well performance conditions.