For most of the 15th century, the Christian empire and the Sultanate of Adal existed in a precarious state of balance, but in the second decade of the sixteenth century, a successful military commander Ahmed Ibin Ibrahim Al Ghazi, (Ahmed Gran, the "left handed"), seized power in Harar which had become the seat of the Sultanate in 1520 CE. Acquiring the status of a religious leader, he called he launched a successful jihad to break the Christian power. After winning a major victory in 1529 CE, his forces ravaged far and wide across the empire for over a decade, destroying much of the literary, architectural, cultural and material wealth of medieval Ethiopia. In 1541, the arrival of a force of Portuguese to help the Emperor Galawdewos led Emir Ahmed to call on support from the Ottoman empire. After a preliminary defeat, the Portuguese helped Galawdewos win victory near Lake Tana in February 1543 where Emir Ahmed was killed. With his death the jihad collapsed as did the power of Adal.
Originally, the Portuguese were mainly concerned to strengthen their hegemony over the Indian Ocean trade routes. They subsequently made every effort to try to persuade Ethiopia to reject its Monophysite version of Christianity and convert to Roman Catholicism. The resulting conflicts, reaching the level of civil war, continued until the Jesuits and all Roman Catholics were expelled in 1632, also contributed to the weakness of an already exhausted empire and its inability to stem the advances by Oromo peoples from the south. The conflicts of the 1520s and the successes of the jihad in the 1530s, together with the collapse of the Sultanates and the Sidama kingdoms opened the way for pastoral Oromo confederacies in the area of the Ganale River to expand north into Bali and Fatajar. Originally the attacks seemed to be largely raids for plunder but once the weakness of opposition became apparent, during the Michelle gada (1554-1562 CE), the Oromo began to settle in the areas they had overrun. From Fatajar, the Metcha-Tulama clans spread out across the south and west, and to the north over the next century. Their original unity fragmented and the confederacies began to disintegrate as they settled. In the east, they destroyed the power of Adal in the latter sixteenth century though the walls of Harar kept the city inviolate. Oromo advances continued north, over-running much of Shoa and advancing into Wollo. To the west and south west they eventually overran Ennarya and advanced as far as the Gojeb River, where they were halted by the powerful kingdom of Kaffa. In the early 1800s, several Oromo kingdoms were set up in the Gibe area: Limmu-Ennarya (about 1800), Gumma, Gomma, Jimma, the most powerful, and Gera.
In the face of the advancing Oromo threat, the weakened empire re-established its center further north, at Gonder north of Lake Tana. This became a permanent capital and the centre of another vigorous flowering of Christian art and culture. As Oromo principalities were established in parts of Shewa and Wollo, their leaders began to play a role in the politics of the Gondar empire. By the end of the 17th century, the Oromo were as much part of the empire as the Amhara or the Tigreans. Their rise was symbolized by the marriage of the Emperor Bakaffa to an Oromo, and during the latter part of the 18th century and the first half of the nineteenth century, the family of Ras Ali Gwangul, ruling in Yejju, played a major role. This was the period of the Zemene Mesafint, the era of the princes, when the imperial power collapsed, and Amhara, Tigrean and Oromo princes fought for control of Gonder and of the emperors. At one point in 1800 there were six crowned emperors alive in the country, each supported by one of the leading regional princes. One emperor was placed on the throne on four different occasions.