The FFII won the Grand Prix 2006 awarded by the Newropeans Magazine in the category "Citizenship - Citizens Action". The award highlights through three different aspects the essential link between European construction and democracy:
1. by rewarding the actors of this European democratisation
2. by having the winners elected by representatives of the European civil society
3. by considering democratization a very concrete process involving European mobility, accessibility and conviviality

In the CNET Networks UK 2005 technology awards, the FFII, together with NoSoftwarePatents.com (a site founded by Florian Müller and now being maintained by the FFII), was the winner in category "Outstanding contribution to software development", because of the "tireless work" that resulted in the rejection of the software patents directive.

In 2005, Mr Jan Macek, member of the FFII Board at the time, was awarded the Brown Cross of Merit, a high distinction offered by the Polish government for outstanding services to Poland. Mr Macek had contributed greatly to Poland's clear no to software patents.