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Recently, inkjet-printed microoptics, such as microlens arrays, have become popular in scientific research as well as industrial applications due to the fast prototyping and production. Naturally, the process parameters have a strong influence on the printed end results. However, optimization of these parameters requires expert knowledge and manual quality control which is subjective and error-prone. To overcome these limitations, we propose an automated evaluation pipeline utilizing both light and confocal microscope images as well as multiple quality measures to quantitatively evaluate the quality of the printed microlens arrays, including the individual microlens radii, sag heights, and focal lengths, as well as the array’s grid parameters.