Glass bottle-manufacturing companies produce bottles of different colors, shapes and sizes. One identified problem is that seeds appear in the bottle mainly due to the temperature and parameters of the oven. This paper presents a new system capable of detecting seeds of 0.1 mm2 in size in glass bottles as they are being manufactured, 24 h per day and 7 days per week. The bottles move along the conveyor belt at 50 m/min, at a production rate of 250 bottles/min. This new proposed method includes deep learning-based artificial intelligence techniques and classical image processing on images acquired with a high-speed line camera. The algorithm comprises three stages. First, the bottle is identified in the input image. Next, an algorithm based in thresholding and morphological operations is applied on this bottle region to locate potential candidates for seeds. Finally, a deep learning-based model can classify whether the proposed candidates are real seeds or not. This method manages to filter out most of false positives due to stains in the glass surface, while no real seeds are lost. The F1 achieved is 0.97. This method reveals the advantages of deep learning techniques for problems where classical image processing algorithms are not sufficient.