With another grant from the French National Centre for Scientific Research (CNRS), he attended courses at the Sorbonne and the École Pratique des Hautes Études to specialize in paleography and in the editing of ancient texts and prints.
In March 1951 he received his doctorate with a dissertation entitled Contribution à l'histoire de l'épistolographie neo-hellénique as the best of his year at the Faculté des Lettres of the University of Paris.
In March 1960 he published a second doctoral dissertation under the title The conspiracy of Sifis Vlastos on Crete (1453–1454) and the new conspiracy movement from 1460-1462 ("Η εν Κρήτη συνωμοσία του Σήφη Βλαστού (1453–1454) και η νέα συνωμοτική κίνησις του 1460–1462”) as the best of his class at the University of Thessaloniki.
That year the Academy of Athens appointed him director of the Hellenic Institute of Byzantine and Post-Byzantine Studies in Venice, a post he held until 1982.
Manousakas' main areas of research were modern Greek epistolography (Frangiskos Skouphos, Greek: Φραγκίσκος Σκούφος), Byzantine and post-Byzantine history, in particular the period of Venetocracy and Cretan Renaissance literature (he discovered an unknown Cretan comedy titled The Forgotten Bride) and paleography (the 574 miniatures in the work of John Skylitzes) and edition philology.