Immediately after becoming shogun, Tsunayoshi gave Hotta Masatoshi the title of Tairo, in a way thanking him for ensuring his succession. Almost immediately after he became shogun, he ordered a vassal of the Takata to commit suicide because of misgovernment, showing his strict approach to the samurai code. He then confiscated his fief of 250,000 koku. During his reign, he would confiscate a total of 1,400,000 koku.
In 1682, Shogun Tsunayoshi ordered his censors and police to raise the living standard of the people. Soon, prostitution was banned, waitresses could not be employed in tea houses, and soon rare and expensive fabrics were banned. Most probably, smuggling began as a practice in Japan soon after Tsunayoshi's authoritarian laws came into effect. In 1684, Tsunayoshi also decreased the power of the tairo after the assassination of Masatoshi by a cousin in that same year.
Nonetheless, due again to maternal advice, Tsunayoshi became very religious, promoting the Neo-Confucianism of Zhu Xi. In 1682, he read to the daimyo an exposition of the "Great Learning," which would become an annual tradition at the shogun's court. He soon began to lecture even more, and in 1690 lectured about Neo-Confucian work to Shinto and Buddhist daimyo, and even to envoys from the court of Emperor Higashiyama in Kyoto. He also was interested in several Chinese works, namely The Great Learning (Da Xue) and The Classic of Filial Piety (Xiao Jing). Tsunayoshi also loved art and the No drama.
In 1691, Engelbert Kaempfer visited Edo as part of the annual Dutch embassy from Dejima in Nagasaki. He journeyed from Nagasaki to Osaka, to Kyoto, and there to Edo. Kaempfer gives us information on Japan during the early reign of Tokugawa Tsunayoshi. As the Dutch embassy entered Edo in 1692, they asked to have an audience with Shogun Tsunayoshi. While they were waiting for approval, a fire destroyed six hundred houses in Edo, and the audience was postponed. Tsunayoshi and several of the ladies of the court sat behind reed screens, while the Dutch embassy sat in front of them. Tsunayoshi took an interest in Western matters, and apparently asked them to talk and sing with one another for him to see how Westerners behaved. Tsunayoshi later put on a No drama for them.
Perhaps owing to mental retardation, or perhaps even religious fundamentalism, Tsunayoshi had an obsession with living things in the later parts of his rule. In the 1690s and 1700s, Tsunayoshi, who was born in the Year of the Dog, thought he should take several measures concerning dogs. A collection of edicts released daily, known as the Edicts on Compassion for Living Things (生類憐みの令) told the populace to protect dogs, since in Edo there were many stray and diseased dogs walking around the city. Therefore, he earned the pejorative title Inu-Kubou (犬公方:Inu=Dog, Kubou=formal title of Shogun).
In 1695, there were so many dogs that Edo began to smell horribly. An apprentice was even executed because he wounded a dog. Finally, the trouble was taken to a distance, as over 50,000 dogs were deported to kennels in the suburbs of the city where they would be housed. They were apparently fed rice and fish which were at the expense of the taxpaying citizens of Edo.
For the latter part of Tsunayoshi's reign, he was advised by Yanagisawa Yoshiyasu. It was a golden era of classic Japanese art, known as the Genroku era.
In 1701, Asano Naganori, the daimyo of Ako han, having been insulted by Kira Yoshinaka in Edo Castle, attempted to kill him. Asano was executed, but Kira went unpunished. Asano's Forty-seven Ronin avenged his death by killing Kira and became a legend that influenced many plays and stories of the era. The most successful of them was a bunraku play called Kanadehon Chushingura (now simply called Chushingura, or "Treasury of Loyal Retainers"), written in 1748 by Takeda Izumo and two associates; it was later adapted into a kabuki play, which is still one of Japan's most popular. The earliest known account of the Ako incident in the West was published in 1822 in Isaac Titsingh's book, Illustrations of Japan.
In 1707, when Mt. Fuji erupted, Shogun Tsunayoshi was already ill, and on February 19, 1709, he died at the age of 62, three days short of his 63rd birthday. He was succeeded by his nephew, Tokugawa Ienobu, who was the son of his other brother, Tokugawa Tsunashige, the former Lord of Kofu, which was a title Ienobu held before becoming shogun.