He is then seen to take the chunks off his head before throwing them out of the carriage window, and later shouting.
Amid the ensuing cacophony a group can be heard singing "he's got bagel on his head".
The footage then cuts to two officers boarding the train, with one asking: "Has anyone seen anything, anyone know who's involved? The train will not move until I find out."
The video also shows brawls in the carriage and outside on the platform. It is not known if these were connected to the bagels.
Using the hashtag #BagelGate, British Transport Police (BTP) tweeted: "Let's be clear, no bagel should be treated so cruelly. And no one subjected to intimidating behaviour. Ever need us text 61016."
A BTP spokesman said officers were called to Potters Bar station at 1.15am after reports of a disturbance on a train.
Officers from Hertfordshire Police attended on their behalf but no allegations of any assault were made and there were no arrests, the spokesman added.
A spokeswoman for Great Northern said: "We take all incidents of intimidating behaviour on our services very seriously and encourage passengers to report them to the BTP. Passengers can also text any incidents to the BTP on 61016."
• This story originally appeared on the Daily Telegraph website