Constantine Monomachos, of a prominent Constantinopolitan family, was recalled from exile on Mytilene to marry Zoe after the mob-enforced deposition of Michael V. His policies generally favored the political and economic elite of the capital; Psellos reports that he opened the Senate to merchants, and he was lavish in his support both of monasteries and of his mistress, Maria Skleraina. While he was able to repel a Rus’ attack on the capital in the first years of his reign, he was charged with neglecting both the provincial and central armies. Constantine did expand the empire slightly by annexing Ani in Armenia in 1045. The situation in the East was changing with the Arab world in decline and the rise of the Seljuk Turks. Byzantines and Turks fought in the mid 1040s but concluded a truce in 1048. In 1042/3 the general George Maniakes led a revolt against Constantine that only ended when George unexpectedly died. In 1047 another general, Leo Tornikes, also rebelled and although he too was defeated, his removal of troops from the Danube frontier opened up the region to Pecheneg raids into the next decade.
Constantine ruled over a brilliant court and patronized a collection of learned men, poets, lawyers, philosophers, and historians; in 1045 Constantine refounded the University of Constantinople. The year 1054 saw the opening salvos in the schism between the eastern and western churches. The old divisions that had arisen during the Photian Schism reappeared as the two sides debated the theory of papal supremacy, and the filioque clause that the western Church had added to the Nicene Creed. Eventually the papal legate Cardinal Humbert excommunicated Patriarch Michael Keroularios, to which Keroularios responded in kind. Although this is not the definitive act that it was once portrayed as, it nevertheless highlights the tensions growing between East and West, as well as between emperor and patriarch. Constantine had hoped for an alliance with the papacy against the Norman threat in southern Italy. Keroularios was to gain great prestige from this point, essentially running the government of Michael VI and playing kingmaker for Isaakios I Komnenos. In economic matters, Constantine's reign saw the continued expansion of aristocratic estates and the first substantial debasement of the Byzantine gold coin—the dollar of the Middle Ages—since its creation seven hundred years earlier. This marked the first step in the loss of international prestige that would characterize Byzantine monetary history for the remainder of the eleventh century.
As with the seals of Romanos III and Michael IV, those of Constantine IX maintain the bust of Christ with the “Emmanuel” inscription on the obverse. The obverse side of Constantine's seals resemble those of his immediate predecessors. The emperor is shown wearing a loros and crown, and holding a globus cruciger and scepter. There are, however, three different obverse inscriptions found on his seals. Constantine is either identified as basileus Romaion (emperor of the Romans), autokrator (sole ruler), or autokrator augustus Romaion (sole ruler and augustus of the Romans).