Article 4 (6) of the GDPR sets the definition for a ‘filing system’. If the personal data that the company processes manually is in structured form and the processing is conducted in a database, then yes GDPR does apply. If the processing is one-off and the company does not use a database, then GDPR might not apply.

Personal Data Breach Reporting Requirements Under the GDPR
What is Data Breach? A personal data breach is security incident that results in the accidental or unlawful destruction, loss, alteration, unauthorized disclosure of, or