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• Knowledge about on-board passenger comfort in public transport vehicles is key to preventing crowding and, in particular, restoring passenger confidence post-COVID-19. • Automatic Passenger Counting systems offer relevant but usually incomplete data due to the high installation costs involved. • A new Kalman filter based estimation method for on-board comfort is proposed, using historical and current non-exhaustive Automatic Passenger Counting data. • The accuracy and reliability of the method are evaluated through application to the tramway network of Nantes, France. • The method is found to deliver good estimation accuracy in terms of both passenger numbers and on-board comfort levels. The prevention of crowding inside buses, trams and trains is an important component of on-board passenger comfort and is central to the provision of good public transport services. In light of the COVID-19 pandemic and the associated significant reduction in public transport patronage and, more importantly, in passenger confidence, the avoidance of crowds by passengers and operators alike becomes even more critical. This is where the provision of information on on-board comfort becomes a necessity. The present study, therefore, proposes a new Kalman filter based estimation scheme for on-board comfort levels, employing historical and current (same-day) non-exhaustive Automatic Passenger Counting data, as well as Automatic Vehicle Locating measurements. The accuracy and reliability of the estimation is, then, evaluated through application to the tramway network of the French city of Nantes. The results suggest that the proposed method is able to deliver good estimation accuracy, both in terms of absolute passenger numbers, but also, more crucially, in terms of on-board comfort Levels of Service. [ABSTRACT FROM AUTHOR]