During the first few months of his rule, al-Mahdi began to consolidate all powers to himself and made drastic changes, especially the financial cells. Previously, Abu Abdullah reserved the gains for the Katama soldiers, but al-Mahdi stripped the fortunes they had gained in the battles. Abul Abbas, the brother of Abu Abdullah, however did not acquiesce but began to criticize al-Mahdi's actions and even did not like the whole power in the hands of al-Mahdi. Qadi Noman states that when Abul Abbas had been made a deputy leader at Raqada, he had acquired a taste for power and was therefore resentful of being compelled to surrender his authority to al-Mahdi and to be merely his subordinate. He exploited the discontent of the Katama chiefs who were losing power under the new administration of al-Mahdi. He also began to instigate his brother, Abu Abdullah and eventually convinced him to some extent to confront al-Mahdi.
It is recounted that once Abu Abdullah dared to suggest al-Mahdi to sit aside with all honours, while he would run the affairs of his state for him in a way that was suitable to the people, for he had known the people for a long time and was aware of their needs and how they should be treated. This gesture warned al-Mahdi of the change that had taken place in Abu Abdullah's character and stand. He however pretended to confess his advice and gave him a gentle answer. When Abu Abdullah wavered in his absolute loyalty, al-Mahdi did not waste much time in eliminating him. Al-Mahdi had his spies planted where both brothers met, and ultimately, both of them were killed on 15th Jamada II, 298/February 18, 911. Al-Mahdi offered the funeral service of Abu Abdullah to glorify his outstanding services and said: "Abu Abdullah was caught in delusion. The real traitor was Abul Abbas."
The executions of Abu Abdullah and Abul Abbas were soon followed by a riot of the Katama tribe which took place immediately after the funeral. Al-Mahdi was not at all frightened and mounted his horse, boldly rode out among the excited crowds and with that personal courage and valour characterized him, told to the rioters, according to "Iftitahu'd-Dawa" (p. 267) by Qadi Noman that: "O'people, you know the status of Abu Abdullah and Abul Abbas in Islam, but satan misguided them, resulting them being deserved for killing. I give you all the security of lives." After hearing this, the people dispersed.
Dr. Zahid Ali (1888-1958), who is not favourably deposed towards the Fatimids, writes however, about al-Mahdi in his "Tarikh-i Fatimiyyin Misr" (Karachi, 1963, 2nd ed., 1st. vol., p. 134) that, "If al-Mahdi had not acted wisely and determinedly at that time to quell revolt of Abul Abbas and Abu Abdullah, the Fatimid state would have disappeared for ever. It was he who made the foundation of the Fatimid dynasty so strong that it could last for nearly two hundred and fifty years. He did not remain content with the territory he got, he expanded its frontiers upto the Black Sea by conquering other parts of Africa. He vanquished the Idrisids and also tried to conquer Egypt but did not succeed. He strengthened his naval fleet thereby increasing the Fatimid marine power so much that it could compete with Byzantine, the strongest naval power of that period. He devised proper administrative measures for every department which resulted in peace in every corner of his country."