The successor of Pope Honorius III (1216–27), he fully inherited the traditions of Pope Gregory VII (1073–85) and of his uncle Pope Innocent III (1198-1216), and zealously continued their policy of Papal supremacy.
He was created Cardinal Deacon of S. Eustachio by his cousin Innocent III in December 1198. In 1206 he was promoted to the rank of Cardinal Bishop of Ostia e Velletri. He became dean of the Sacred College of Cardinals in 1219. He was also archpriest of the patriarchal Vatican Basilica (1198 until 1207) and the second Cardinal Protector of the Order of Franciscans.
As Cardinal Bishop of Ostia he had been in the inner circle of Honorius III, and associated with the Pope's policy of accommodation with the formidable Hohenstaufen Emperor Frederick II (1220–50), whose lawyers in Naples and Capua asserted his position as universal temporal ruler, in the mold of Constantine.
Although peace was thus secured (August 1230) for a season, the Roman people were far from satisfied; driven by a revolt from his own capital in June 1232, the Pope was compelled to take refuge at Anagni and invoke the aid of Frederick II. Gregory IX and Hohenstaufen came to a truce, but when Frederick II defeated the Lombard League in 1239, the possibility that he might dominate all of Italy, surrounding the Papal States, became a very real threat. A new outbreak of hostility led to a fresh excommunication of the emperor in 1239, and to a prolonged war.
Gregory IX denounced Frederick II as a heretic and summoned a council at Rome to give point to his anathema, at which Frederick II attempted to capture or sink as many ships carrying prelates to the synod as he could. The struggle was only terminated by the death of Gregory IX on August 22, 1241. He died before events could reach their climax; it was his successor, aptly named Pope Innocent IV (1243-54) who declared a crusade in 1245 that would finish the Hohenstaufen threat.
This pope, being a remarkably skillful and learned lawyer, caused to be prepared Nova Compilatio decretalium, which was promulgated in numerous copies in 1234. (It was first printed at Mainz in 1473). This New Compilation of Decretals was the culmination of a long process of systematising the mass of pronouncements that had accumulated since the Early Middle Ages, a process that had been under way since the first half of the 12th century and had come to fruition in the Decretum compiled and edited by the papally-commissioned legist Gratian and published in 1140. The supplement completed the work, which provided the foundation for papal legal theory.
His Bull Parens scientiarum of 1231 resolved differences between the unruly university scholars of Paris and the local authorities, who had precipitated this crisis by high-handed actions. His solution was in the manner of a true follower of Innocent III: he issued what in retrospect has been viewed as the magna carta of the University, assuming direct control by extending papal patronage: his Bull allowed future suspension of lectures over a flexible range of provocations, from "monstrous injury or offense" to squabbles over "the right to assess the rents of lodgings".
Gregory IX believed the problem of heresy needed serious attention and was not content with leaving it to the bishops, who might have been lax, but extended central control in this essential area as well. In 1231, he established the Papal Inquisition to deal with it, although he did not approve the use of torture as a tool of investigation or for penance.
He appointed ten cardinals and canonized Saints Elizabeth, Dominic de Guzmán, and Anthony of Padua, and also Francis of Assisi, of whom he had been a personal friend and early patron. His encroachments upon the rights of the English Church during the reign of Henry III of England (1216-72) are well known; similar attempts against the liberties of the national church of France were supposedly the occasion of the Pragmatic Sanction of Louis IX of France (1226-70), now generally thought to be a 14th-century forgery.
Gregory IX was a principal figure in the cementing and institutionalizing of Church teaching that discriminated against Jews and condemned them to an inferior status in Christendom. In the 1234 Decretals, he invested the doctrine of perpetua servitus iudaeorum – perpetual servitude of the Jews – with the force of canonical law. According to this, Jews would have to remain in a condition of political servitude and abject humiliation until Judgment Day. The doctrine then found its way into the doctrine of servitus camerae imperialis, or servitude immediately subject to the Emperor's authority, promulgated by Frederick II. The second-class status of Jews thereby established would last until well into the 19th century.
He transformed a chapel to Our Lady in the church of Santa Maria del Popolo in Rome.
Gregory IX endorsed the Northern Crusades and Teutonic Order's attempts to conquer Orthodox Russia (particularly the Pskov Republic and the Novgorod Republic). In the year 1232, Gregory IX requested the Livonian Brothers of the Sword to send troops to protect Finland, whose semi-Pagan people were fighting against Novgorod Republic in the Finnish-Novgorodian wars, however, there is no known information if any ever arrived to assist.