Emperor Maximilian I granted Emden its town privilege and coat of arms in 1495. The arms depict a small angel standing on a city wall — Engelke up de Muer in the local Low German, the Little Angel on the Wall — a figure that still appears on civic stationery and town gates. The exact founding date is older and unknown. Eighth-century records mention a place called Amuthon in this area, almost certainly the seedling of the modern town. What gave Emden its sudden international weight was the Reformation. Countess Anna von Oldenburg, ruling here in the 1540s, attempted to chart a Protestant third way between Lutheranism and Catholicism. In 1542 she invited the Polish reformer John Laski to pastor an Emden congregation, and for seven years he made the town a working laboratory of Reformed Christianity before imperial pressure forced him out. The Synod of Emden in 1571 is generally taken as the founding moment of the Dutch Reformed Church.

By the late sixteenth century Emden was prospering on the Dutch Revolt. The Spanish blockade of Flemish and Brabant ports had collapsed the maritime trade of Antwerp and Bruges, and the cargoes redirected to Emden, the nearest unobstructed harbor. Protestant refugees poured in from Flanders and Brabant. Brabantian Dutch became the official language of trade and civil administration. The Emden Revolution of 1595 effectively made the town a self-governing city-state under Dutch protection. For most of the seventeenth century it was, in language and politics, more Dutch than German — a peculiarity that still surfaces in the old town's gabled brick architecture, the Dutch family names in the cemetery, and the location of the Johannes a Lasco Library, named for the Polish reformer who started it all.

On 6 September 1944, in one of the heaviest single raids on a German city of its size, RAF Bomber Command leveled most of central Emden in a single night. Eighty percent of the medieval town was destroyed. The harbor, the rail yards and the town hall went down together. After the war, under Allied occupation, the slow work of rebuilding began. The current town hall opened on 6 September 1962 — exactly eighteen years after the raid, to the day. The deliberate choice of date was a quiet statement: not a memorial, exactly, but an insistence that the calendar belonged to the survivors. The new building incorporated salvaged elements from the original. The angel went back on the wall.

Modern Emden runs on two industries that would have astonished its sixteenth-century merchants. The Volkswagen plant on the western edge of town, opened in 1964, employs about 7,700 people and builds the all-electric ID.4 and ID.7 — the plant completed its transition to electric-only production at the end of 2024. Emden is one of the three main car-shipping ports in Europe — alongside Zeebrugge and Bremerhaven — and more than 1.4 million vehicles passed through its terminal in 2017. Across the harbor sits the Nordseewerke shipyard, a ThyssenKrupp subsidiary that builds conventional submarines for export customers along with cargo ships, icebreakers and dredgers. The yard's diving submarines are sold worldwide. Few visitors realize that the same harbor exports family hatchbacks and military submarines side by side, often within the same week.

For a town of fifty thousand, Emden produces an outsized share of national figures. The comedian Otto Waalkes, born here in 1948, is one of postwar Germany's best-known comic performers — his rubber-faced routines have been a fixture of German television for fifty years, and his cartoon character Ottifant is a national mascot. The film director Wolfgang Petersen, born in Emden in 1941, directed Das Boot, The Neverending Story, Air Force One and The Perfect Storm. The publisher Henri Nannen, born here in 1913, founded Stern magazine in 1948 and ran it for nearly four decades. The Kunsthalle Emden — the town's modern art museum — was originally Nannen's private collection, and remains one of the strongest regional galleries in Lower Saxony. Otto, Wolfgang and Henri: a comedian, a filmmaker and a publisher, all coming up from the same flat coast on the Ems.