Iemitsu reinforced Japan's strict class system, which placed samurai (led by the daimyo) at the top, followed by farmers, artisans, and merchants, and sought to maintain stability through a rigid societal order. In an attempt to reign in the power of the daimyo,Tokugawa Iemitsu instituted the sankin-kotai system, requiring the daimyo (feudal lords) to spend alternating years at the shogun’s court in Edo (modern-day Tokyo), forcing them to spend large sums maintaining two residences and traveling. Their families were also kept in Edo as virtual hostages to ensure their loyalty. This system limited the resources of the daimyo and their ability to build independent power bases in their territories. He also made changed to the Buke Shohatto (Laws for the Military Houses), forbidding the daimyo from fighting, forming alliances, or swear oaths to one another. The daimyo needed the shogun’s approval for marriages, fortifications, and even travel; and foreign trade and travel were strictly regulated by the shogun. 

Iemitsu also sought to reign in foreign influences. In the 1630s he enacted the sakoku policy, which ended the red seal trade voyages and prohibited overseas travel by Japanese. Trade with Asian countries such as China and Korea continued, but it was controlled. The Dutch East India Company was the only Western power that could trade with Japan and only at the port of Nagasaki. Iemitsu also increased the suppression of Christianity, which he saw it as a political and ideological threat to the unity of Japan and the loyalty of his subjects, particularly the Christian daimyo. This culminated in the Shimabara Rebellion (1637-1638), a Christian-led uprising that was brutally suppressed by the shogunate. Christians were forced to go underground, becoming "Hidden Christians." 

While Iemitsu reduced the power of the daimyo, he could not completely eliminate their influence. The daimyo retained local control over their domains, and in many regions, they still had significant authority over their own military forces, laws, and economic policies. The alternate attendance system also placed a financial burden on the shogunate, as maintaining the infrastructure for constant travel and overseeing the daimyo’s movements required significant expenses. Some samurai also began to suffer. Many samurai became impoverished over time due to the lack of wars and the decreasing revenue collected by samurai landowners, which led to discontent among some samurai who had lost their traditional military roles and economic security.

The frustration of the with the shogunate was displayed in the Keian Uprising of 1651, when a number of ronin (masterless samurai) attempted to take advantage of Iemitsu's death and launch a coup. The conspirators aimed to force the shogunate to relax its policies of seizing the estates of daimyo, which under Iemitsu had deprived tens of thousands of samurai of position and income, adding them to the ranks of rōnin. Ultimately the coup failed, but the shogunate did reduce its confiscation of estates and worked to help ronin find permanent jobs. The Keian uprising was followed by another uprising of ronin, and indicating that the rising number of wandering ronin would continue to be a problem.