The domain's location close to Korea and far from Edo, the shogunal capital, along with its trade connections, brought significant foreign influence to the area. The area was a center for ceramic production and techniques as a result of its connections with Korea, becoming famous for its Imari porcelain which was a significant export good to Europe. The area also bore a considerable Christian peasant population, which erupted in protest in the famous Shimabara Rebellion (1637-8). Towards the end of the Tokugawa period, elements within Saga sided with groups from Tosa, Satsuma, and Chōshū against the shogunate. Saga leaders would later turn against the new Meiji government, launching the Saga Rebellion in 1874, which ultimately failed.
The shogunate imposed upon Saga responsibility for defense of the port of Nagasaki and enforcement of the maritime restrictions (kaikin). Though this burden was shared with the Fukuoka Domain, each domain bearing these responsibilities in alternate years, it nevertheless frequently strained Saga's finances. As a result, it was not unknown for Saga to seek to lessen its losses by reducing the number of samurai it sent to defend the port. In October 1808, when the HMS Phaeton created an incident, capturing Dutch merchants and threatening Japanese and Chinese ships in the harbor, only 100 Saga samurai were present to deal with the situation, rather than the obligatory one thousand. As no further troops could be summoned to the port in time, the shogunate was forced to submit to the demands of the British ship, and scolded Saga harshly for its failure to fulfill its obligations. The domain would be further weakened by a typhoon in 1828 which cost Saga approximately 10,000 lives.
Saga recovered in the last decade or so of the bakumatsu period (i.e. the 1860s), however, taking in Western technology and reforming the domain's governance. The bureaucracy was cut by 80%, and efforts were made to support and encourage the peasantry. The domain's economy came to be focused upon ceramics, tea, charcoal, and related goods, and prosperity was found through trade.
The tenth lord of Saga, Nabeshima Naomasa (r. 1830-61), established organizations for the research of Western technologies, including steel refining, steam engines and artillery, and turned the domain's efforts towards these pursuits, making it one of the most modern domains in this period. Saga thus began operations at the first Japanese iron refinery in 1849, and made the first use of reverberatory furnaces three years later. In 1853, Russian Admiral Yevfimy Putyatin arrived in Nagasaki harbor, and provided the first demonstration of a steam locomotive to the Japanese. Ishiguro Hirotsugu, Nakamura Kisuke, and Tanaka Hisashige were among the first Japanese engineers, who attempted to manufacture their own steam locomotives and steamships.
When the shogunate relaxed the restrictions on the construction of large ships, an order was placed with the Dutch. Saga saw the revitalization of Japans' shipbuilding industry, and the launching of the first Japanese steamship, the Ryōfūmaru. The Nagasaki naval academy was established in 1855, its first students coming from Saga. By 1866, the incorporation of British Armstrong Whitworth cannon made the ships at Nagasaki into the first Japanese Western-style ("modern") navy. The defense batteries at Shinagawa were also supplied by cannon from Saga.
Largely responsible for Japan's technological and military advancement, and holding much of the fruits of those labors, Saga attracted the attention of the shogunate, which kept a close eye on the domain until its fall in 1868. Saga played an important role in the Meiji Restoration, alongside the domains of Tosa, Satsuma, and Chōshū, and samurai from the domain fought the shogunate at the battle of Ueno and in other clashes of the Boshin War. As a result, the new Meiji government which emerged afterwards featured a number of figures from Saga, including Etō Shinpei, Ōkuma Shigenobu, Ōki Takatō, and Sano Tsunetami. Etō resigned from the government, however, along with a number of others in 1873 as the result of extensive disputes over invading Korea, an action which he, Saigō Takamori and others supported, but which was ultimately rejected by the council. Etō then organized the Saga Rebellion the following year, leading 3000 men in an assault against the new government which was quickly suppressed.