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Background Working environment should not present a risk of injury or disease but many thousands of workers worldwide remain exposed to hazardous substances particularly in developing countries. Flour dust is one of those hazardous substances to which the flour mills workers are exposed to, inhalation of flour dust may cause diverse lung diseases with different severity of symptoms ranging from simple irritation to allergic reaction and chronic respiratory disorders, including asthma. Therefore, the present study was done to detect the prevalence of respiratory problems among flour mills workers. Methods The study was carried out in the flour mills of Assiut, it was a cross-sectional study among 203 workers. The study instruments were a semi-structured questionnaire about respiratory symptoms, chest examination and pulmonary function tests (PFT). Results The age of the study workers ranged from 19 to 60 years old, 94.1% were males, 50.7% were from urban regions. Pulmonary function abnormalities were found in 36.4% of them and 20.7% were diagnosed with bronchial asthma. Significant relationships were detected between abnormal pulmonary function tests and workers ≥ 40 years old, low educational level and those who worked in the flour mills for ≥ 10 years. Conclusions Flour dust cause respiratory symptoms and impair the pulmonary function of the flour mills workers and they may develop bronchial asthma which affect their work efficiency. Recommendations Medical care must be provided regularly to the flour mills workers and safety measures are mandatory. Trial registration ClinicalTrials.gov. NCT03678519. Registered August 10, 2022.