Ali reorganized the administration. He appointed Governors and administrators for various provinces and districts. He appointed Qazis for the various cities. He issued instructions requiring his officers to administer justice with a stern hand. He asked the tax collectors to be prompt in the collection of taxes. They were; however, warned not to adopt oppressive measures. He exhorted his officials to be scrupulously honest. He asked all concerned to do their duties diligently and conscientiously. He wanted that law and order should be maintained strictly. That all miscreants should be rounded up and suitably punished. He brought home to all concerned that he would not tolerate any dereliction of duty on the part of any official high or low. He emphasized the need of promoting Islamic values.
The plan of Ali was that soon after the victory of Basra when the morale of his forces was high, he should invade Syria and bring Muawiyah to his knees. Ali soon found that there were difficulties in the materialization of such plan. The Bedouins of Kufa were once again at their game of creating discontent against the established authority. In the Battle of the Camel, in spite of the victory of Ali, many persons of Kufa had been killed. There was hardly any family which had not lost someone in the battle. The people of Kufa mourned the death of such persons, and they were not inclined to risk another war. At Basra, Ali had prohibited his men to pillage Basra, enslave the Basrites or, plunder their property. The Battle of Basra had not brought any material gain to the people of Kufa, and they were reluctant to undertake another campaign, unless they were assured of some material advantage.
Ali appointed his relatives and friends as the Governors of some provinces. Ashtar, the Bedouin leader of Kufa, stirred trouble by criticizing Ali for such appointments. To the people of Kufa he said, "What benefit has accrued to us in shedding the blood of Othman for his favoritism when his successor is to indulge in the same practice?" Those who mourned for the deaths of their dear ones in the Battle of Basra posed the question, "What have we gained in fighting against the Mother of the Faithful?" Thus hardly had Ali begun his rule in Kufa when the embers of discontent began to smolder in the capital city. The irony of the situation was that Ali had hardly any military force at his disposal which he could put into the field by his order. He had to raise volunteers for any action and the people had their own moods. The initiative had thus came to rest with them, and they dictated terms subject to which they would fight. By shifting the capital from Madina, Ali could not expect much help from Madina or Makkah, and he had to depend heavily on the people of Kufa. The difficulty with the people of Kufa was that they would not fight for a cause; they could be induced to fight only for some material advantage.
The difficulties of Ali increased when trouble began in the province of Seestan. The trouble was created by the followers of Abdullah b Saba, the man who had led the revolt against Othman. The extremist section among these rebels considered that there was no fun in killing one Caliph when he was to be succeeded by another Caliph. The aim of these rebels was that they should capture power for themselves, and set up an independent state. When Ayesha had captured, she had executed all such Basrites who were involved in the assassination of Othman. Although Ali defeated the confederates yet he had taken no action to avenge the death of those Basrites. The followers of Ibn Sabah raised the cry for the vengeance for the execution of these parties. They gained ascendancy in Seestan, which province broke into open revolt, and refused to pay taxes. Ali sent a force from Kufa to put down the revolt. The force of Ali suffered defeat. Another force sent from Kufa met a similar fate. It appears that there was some treachery in the ranks of the force of Ali. Ali thereafter raised another force from Yemen, and other parts of the empire and sent it to Seestan under the command of Abdullah b Abbas, the Governor of Basra. This time the rebels were defeated, and the revolt was suppressed. The campaigns in Seestan affected the prestige of the caliphate, and proved to be a great strain on the already meager resources at the disposal of the caliphate. In the campaign against Seestan much time was lost, and this loss of time worked to the advantage of Muawiyah and the disadvantage of Ali. According to one account the trouble in Seestan was created by the agents of Muawiyah who had no scruples in making common cause with the murderers of Othman.