The centre of Como was badly hit after Lake Como flooded following intense rainfall, with water flowing through the city's streets, partially submerging cars and causing damage to homes and businesses.
"The club will donate all the proceeds from the Italian Cup match against Sassuolo... to support the local community during this difficult time," Fabregas said in an Instagram post referring to the second-round tie between the two Serie A teams.
"My thoughts are with everyone in Como today. Seeing our beautiful lake flood and the damage it has brought is heartbreaking," he added.
"Como is more than just a city to me, it is home, it is family, it is community.
"To all the people, families, and businesses affected, please know you are not alone," Fabregas said.
The former Spain midfielder ended his playing career at Como in 2023, with the club competing in Serie B, and began his managerial career there, helping them gain promotion as assistant coach and taking over as manager last season.