Little is known of Quimper's family. In 1792 El Mercurio Peruano, a publication of the Sociedad Académica de Amantes de Lima, published a letter he had apparently written to a brother in Lima during his 1790 stay at Nootka Sound.
The Spanish court was becoming increasingly concerned about British and Russian incursions along the Pacific Northwest coast of North America. Seven of the best Spanish naval officers were dispatched to learn of British and Russian intentions. These included Quimper and his fellow Peruvian Juan Francisco de la Bodega y Quadra, who was named commander of the Marine Department of San Blas. They departed from Cadiz aboard the San Ramon in May 1789. Shortly after their arrival at Veracruz, the seven were transferred to San Blas.
In July 1789 they received news from the Pacific Northwest with the arrival of the Princesa Real, a fur-trading vessel captured from the British at Nootka Sound by Spanish commander Esteban José Martinez. In 1788 the British exporer John Meares had established a fur trading post on Nootka Sound. Martinez considered this settlement illegal and had seized the port and some vessels, including the Princess Royal which he renamed the Princesa Real and dispatched to San Blas at the disposition of New Spain Viceroy Revillagigedo. The Viceroy, however, wished to avoid further difficulties with the British and ordered Quimper to return the vessel.
On February 3, 1790, a Spanish expedition sailed north from San Blas under the command of Captain Francisco de Eliza. It included Lieutenants Francisco Eliza and Salvador Fidalgo, and Sub-Lieutenant Manuel Quimper. Their purpose was to strengthen the settlement at Nootka Sound, to further chart the waters of the Strait of Juan de Fuca and the San Juan Islands, and to return the Princesa Real to the British. After several weeks at sea, the Princesa Real and Quimper arrived with difficulty at Nootka Sound where repairs on the vessel were untertaken before returning the ship to the British. Throughout the month of May the Princesa Real was repaired with no sign of the British. Quimper then used the vessel to carry out a two-month exploration of the north and south coasts of the Strait of Juan de Fuca.
During June and July he charted and named many geographic features along the south shore of Vancouver Island and the north coast of the Olympic Peninsula. He was the first European to report seeing Mount Baker, which he named La Gran Montagna Carmelita. On the Olympic Peninsula he traded with and observed the customs of indigenous people near Dungeness (which he named Bahia de Quimper) and near the Elwha River, which were most likely members of the Klallam tribe in both instances and he was possibly the first European they had seen. Most of his discoveries along the strait were renamed by British Captain George Vancouver in 1792. Those which retained at least a semblance of his Spanish names include Port Angeles, Rosario Strait, Quimper Peninsula and Fidalgo Island.
Quimper returned to Nootka Sound in early August but was unable to enter the port for several days due to heavy fog. He set sail for New Spain and arrived at Monterey on September 1, 1790. From there he was joined by Lt. Fidalgo aboard the San Carlos. They arrived at San Blas on November 13, 1790. Viceroy Revillagigedo was surprised to learn that the Princesa Real was still in Spanish possession. He dispatched a message to the Court in Madrid recommending the return of the vessel to the British at Macau and sent a report of Quimper's explorations in the Pacific Northwest with nine of his charts. Quimper was promoted to Frigate Lieutenant.
On February 14, 1791, Quimper set sail aboard the Princesa Real with orders from San Blas commander Juan Francisco de la Bodega y Quadra to chart the Sandwich Islands and then turn the vessel over to the Philippines Governor-General Félix Berenguer de Marquina, who would then have it returned to the British at Macau. While exploring the Sandwich Islands he had a tense encounter with James Colnet, the British commander at Nootka, on April 1, 1791. Colnet demanded an explanation from Quimper as to why the Princesa Real had not yet been returned to the British and Quimper informed him of the plans to return it at Macau. Colnet threatened to seize the ship then and there, but when he observed Quimper preparing for combat he backed down. Quimper continued his exploration of the islands of Hawaii, Maui, and Oahu, and on April 19, 1791, set sail for the Philippines.
Quimper arrived at the Cavite naval base on Manila Bay on June 4, 1791. He handed over the ship to Vicente Llanos y Valdés, a relative of the Minister of the Navy. The Princesa Real was returned to Macau on August 12, 1791, but a strong hurricane soon struck there badly damaging the ship, and it was later sold for salvage. Spanish explorer Alessandro Malaspina returned to Manila from his exploration of the Marianas Islands and Quimper helped to create charts of his findings.
On May 21, 1792, Quimper was given command of the frigate San José de las Ánimas and sailed for San Blas, accompanied by the schooner Valdés under the command of Lt. Cosme Bertadano. The two vessels were soon separated by a hurricane causing the Valdés to return to Manila. Quimper continued on to San Blas. His ship was badly damaged by the weather and he did not arrive until nearly six months later on November 6, 1792. He learned that on October 16, orders had been issued granting him permission to marry Francisca Márquez, and appointing him as special assistant to his countryman and friend Juan Francisco de la Bodega y Quadra, the naval commander at San Blas, who was in failing health but did not want to resign his command while the international situation was deteriorating and war was likely. He held this position until February 1794 when Bordega y Quadra died.
Quimper himself was in poor health and was therefore granted permission in June 1795 to return to Spain. While waiting at Veracruz to embark on this voyage he was named the captain of the corvette Atrevida and sailed on this ship to Cádiz while it was still under the command of Malaspina. Quimper apparently never took command of the Atrevida because while it was at the port of Cádiz, he requested and was granted a transfer to Madrid to attend to personal matters. Eight months later he was inducted into the prestigious Orden Militar de Calatrava.
Quimper then served at Algeciras under the command of Bruno de Heceta, a veteran explorer who had also explored the Pacific Northwest of America. He soon asked for the governorship of Guayaquil, but was instead given command of the naval fleet at Madrid, a position he maintained until 1802. He was then appointed the Minister of the Treasury in Veracruz and so returned to America in a ministerial position.
Manuel Quimper was appointed in 1802 a Spanish treasury minister to oversee emperial disbursements in Veracruz. In 1805 he was appointed the governor of Huamanga (later renamed Ayacucho) in the southern part of his native Peru, but due to a confusing incident involving the newly appointed Viceroy of Peru, José Fernando Abascal y Sousa, he instead became the governor of the Peruvian region of Puno on Lake Titicaca.
During his term as governor of Puno an independence movement emerged of which Quimper warned Viceroy Abascal in July 1809. Quimper's own carefully guarded collection of papers, maps, manuscripts, and books were destroyed in an uprising of the local people. He was removed as governor at the end of January 1810. His successor, Manuel Antonio Nieto, died within months and Quiimper returned to Puno as governor in June 1810.
Following the 1814 uprisings for independence in Upper Peru, Quimper was again appointed the governor of Huamanga in August 1814. His journey to his new post, however, was interrupted by a rebellion in the Cuzco region of Peru and he was detoured to the city of Arequipa. From there he and 250 men went to the aid of Puno on December 9, 1814. After restoring order they marched to his natal city of Lima. Quimper was still in Lima when the Viceroy was replaced by Joaquin de la Pezuela, who confirmed his appointment as governor of Huamanga and Quimper traveled there to assume the position that he held for three years before returning to Spain in retirement.
While Quimper was in Spain, his son Colonel Manuel Quimper, was fighting for the Spanish cause in Peru. He had been serving in Upper Peru until named the commander-in-chief of Spanish forces of the southern coast of Peru on February 9, 1820. The young Manuel Quimper suffered a major defeat while defending the city of Nazca and was forced to flee to the coast in October 1820.
Meanwhile in Madrid the senior Quimper received the military honor of La Cruz de San Hermenegildo in 1820. Quimper also began to receive recognition for his literary talent. In 1821 Imprenta Alvarez published his 180-page manuscript of Décima poetry entitled Laicas vivacidades de Quimper, antorcha peruana, acaecimientos del Perú en civiles guerras, promovidas por el Reino de Buenos-Ayres, desde el año 1809 hasta el de 1818, describing his personal observations of the civil wars in Peru from 1809 to 1818.
Still showing regret over the loss of the documents which had been destroyed at Puno, at the end of 1821 he solicited the endorsement of José Bustamente, the director-general of the National Armada, for the publication of a recounting of his experiences aboard the Atrevida in Manila Bay thirty years earlier. He apparently received no support from Bustamente. Nevertheless, in 1822 Quimper published in Madrid his book Islas Sandwich: Descripción sucinta de este archipiélago, which had been previously published in El Mercurio Peruano. In the "Introducción" to this book he attempted to explain himself and his return to Spain, citing his naval service to Spain since adolesence, and the fact that he had been treated as an American in Spain, and as a Spaniard in Peru.
Quimper longed to return to his native land of Peru and in February 1822 took steps to assure sympathetic treatment there upon his return. He returned shortly thereafter and is reported to have become a Peruvian "Patriot" in 1823. The government of the Republic of Peru named him a naval commander in 1827 and later a captain. He continued his literary pursuits and wrote the poem Poema raro, segments of which were published in La Gazeta de Lima. He died in Lima in April 1844.