Imperial vicar in Tuscany
As he did with his other illegitimate offspring, the emperor employed Frederick in various administrative and military functions from a young age. Frederick's ambit was central Italy, and he was appointed imperial vicar general in the March of Ancona in late 1244 or early 1245, when he could not have been much more than twenty years old. After a brief stint at Pontenure with the army of his half-brother Enzo, he was knighted by his father in July 1245 by a Cremona. Between February 1246 and November 1248 he was vicar general in the March of Tuscany and the Papal territory in Tuscany: "in Tuscany from Amelia to Corneto and for all the coast", probably as far south as Ostia. Thereafter until the end of 1250 his vicariate was limited to Tuscany and excluded the Papal territory, which was placed under the vicar Galvano Lancia, father-in-law of Frederick's son Conrad.
Frederick's rule in Tuscany was heavy-handed, but effective. He conscripted soldiers—including Bolognese students and merchants of the Guelph party—and levied taxes from all the cities of Tuscany, most notably Siena, to which he temporarily transferred the silver mines of Montieri as partial compensation for his exactions. In Florence, the chief city of Tuscany, internal conflict between the Guelph and Ghibelline parties allowed the emperor to install Frederick as imperial podestà there (February 1246). His appointment was understood by Vita da Cortona, the biographer of Florentine holy woman Umiliana de' Cerchi, as a fulfillment of her prophecy about the coming of a tyrant. Umilian herself died shortly after Frederick's arrival in the city. Initially, Frederick attempted to reconcile the two parties, but in the end resorted to removing the Guelph capitani del popolo and in early 1248 had the city exile the Guelph leaders and destroy their homes. While he was away on his frequent military campaigns, Frederick delegated his podesteria to vicars.
During his government of Tuscany, Frederick was constantly on the move. He can be shown to have visited staunchly loyal Siena, as well as the traditionally Ghibelline towns of Arezzo, Borgo San Genesio, Fucecchio, Poggibonsi, Prato, San Miniato and San Quirico d'Orcia. His military campaigns took him to Orbetello and Magliano in November–December 1246, to Castiglione del Lago and Perugia in May–June 1247, to the county of Orvieto in the autumn of 1247, to the Lunigiana some time between the summers of 1246 and 1247 and as far as Umbria and the Maremma between the summer of 1249 and spring of 1250.
In March 1247 Frederick met his father in Siena while the latter was on his way to Lyon to meet Pope Innocent IV. A general uprising diverted the emperor, and Frederick went north in August to join the siege of Parma. This was the only time during his vicariate that he ventured north of the Apennines. At Parma he met his half-brother Enzo and his father's other loyal supporters—Manfredi Lancia, Oberto Pelavicino, Ezzelino da Romano, Pietro Ruffo and Taddeo da Sessa. At Parma he was also formally enfeoffed as count of Albe, his father-in-law's old benefice. He had to return swiftly to Florence, however, to prevent it from falling under the control of the Papal legate Ottaviano degli Ubaldini.
After defeating the Florentine uprising in the summer of 1247, the loyalty of even the Ghibelline centres was pragmatic rather than ideological. A second Florentine rebellion in the summer of 1250 defeated his troops near the loyal town of Figline. Frederick's representatives were chased from the city and a new government, called the Primo Popolo (First People), was instituted in Florence. When Emperor Frederick II died on 13 December 1250, although Frederick and Galvano Lancia learned of his death within a week (between 18 and 20 December), most of the imperial officials in Tuscany abandoned their posts. His administration having collapsed, Frederick nonetheless remained in Tuscany until the autumn (1251).