Dozens of the banners, which include a picture of the Pope frowning, have been discovered around the Italian capital over the weekend, prompting council workers to swiftly cover them up.
They criticise the pontiff's intervention into a row involving contraception distribution programme linked to a lay Catholic order.
The posters accuse the pontiff of "decapitating" the Knights of Malta, referring to him asking for the resignation of grand master Matthew Festing last month.
The Pope intervened after Mr Festing dismissed a senior member of the order, Albrecht von Boeselager, after it emerged a condom distribution programme in Myanmar had happened under his watch.
The posters also accuse Pope Francis of "ignoring cardinals", an apparent reference to the him effectively side-lining the Vatican's liaison with the order, Cardinal Burke.
Cardinal Burke publicly challenged the pope last year over his decision to ease Communion restrictions on divorcees who remarry outside the Church.
In a statement seen by Reuters, Father Antonio Spadaro, a Jesuit who is close to the pontiff, said the posters illustrated how Francis was doing well in his role and therefore upsetting many people.