The chapel's priest, Miguel Fernando García López, discovered the graffiti on Wednesday morning and called the police, who have launched an investigation into the incident.
The pews, religious statues, confessional, walls and tabernacle were "covered with red splotches", according to Spanish daily El Mundo.
The slogans, "free abortion", "secular education" and the symbol representing transgenders were daubed in red paint on the chapel walls.
It is the first such case of vandalism in the university's chapel.
Police sources said that those responsible left several posters at the scene but it is unclear whether these give any clue as to their identities.
The outside of the chapel was also vandalized, with "free abortion" daubed across the wall and the lock to the chapel's door broken.
The Autonomous University of Madrid was founded in 1968 and notable alumni include Spain's King Felipe, who studied Law at the university.