With the hot liquid causing a strong electrical burning smell and smoke rising from the panel, the captain chose to divert, the report from the Air Accidents Investigation Branch (AAIB) said.
The hot liquid damaged an audio control panel, producing an electrical burning smell and smoke, an accident report revealed.
According to the bulletin, the manufacturer of the aircraft-in this case, an Airbus A330-243-recommends that pilots use the cup holder.
The AAIB report adds: "The operator also issued a flight crew notice reminding pilots to be careful with liquids".
Airbus rules recommend that crew use cupholders provided when drinking beverages in the cockpit, however the size of cups made it hard for them to be grasped when in the holder. The jet was west of Ireland flying over the North Atlantic Ocean when a pilot's coffee was knocked into the jet's control panel.
The Air Accidents Investigation Branch said there were no injuries and that the airline had since changed its procedures to ensure cup lids are provided for flights on all routes.
A spokeswoman for the airline, which is a subsidiary of Thomas Cook Group, said: "Flight DE2116 from Frankfurt to Cancún on 6 February 2019 diverted to Shannon airport as a precautionary measure due to a minor amount of smoke in the cockpit after a liquid spillage".
The flight continued by way of Manchester, because of the crew's legal operating hours, after the plane was inspected and repaired. Condor said in its statement that the airline "comprehensively investigated" the situation and has since gone over the procedures for liquid in the cockpit. "We apologize for any inconveniences the diversion might have caused to our guests".