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The 13th century conquest of Estonia was undertaken by the Livonian Order, the Kingdom of Denmark, and their allies against the pagan peoples of Estonia (Maavald) around the eastern shores of the Baltic Sea, one of the last corners of medieval Europe to be Christianized. After the success of this Northern Crusade, the German-occupied territory was divided into the Livonian Confederation by William of Modena, while Denmark controlled northern Estonia.

Livonian Brothers of the Sword.

Pope Celestine III called for a crusade against pagans in Northern Europe in 1193. At the beginning of the 13th century, German crusaders from the northern Holy Roman Empire established the stronghold of Riga (in modern Latvia) and formed the Livonian Brothers of the Sword, or Livonian Order. Bishop Albert of Riga founded the Order to aid the Bishopric of Riga in the conversion of the pagan Curonians, Livonians, Semigallians, and Latgalians in Livonia and Courland along the Gulf of Riga. From its foundation the undisciplined Order tended to ignore its supposed vassalage to the bishops.

The indigenous Livonians (Livs), who had been paying tribute to the East Slavic Principality of Polotsk, at first considered the Low Germans as useful allies, but as the German grip tightened, the Livonians under their quasi rex Caupo of Turaida took up arms against the crusaders. The Livonians were defeated and their Rurikid leader Vyachko was taken prisoner in 1206.

The Germans turned their attention to the Latvian tribes to the east in Latgalia. By 1208, the Germans were strong enough to begin operations against the Estonians (maarahvas), who were at that time divided into eight major and seven smaller elderships, which were led by elders with limited co-operation with each other. With the help of the newly converted local tribes of Livs and Letts in 1208, the crusaders initiated raids in Sackalia and Ugaunia in Southern Estonia. The Estonian tribes fiercely resisted the attacks from Riga and occasionally sacked territories controlled by the crusaders. In 1208-27, war parties of the different sides rampaged through Livonia, Latgalia, and different Estonian counties, with the Livs and Latgalians as varying allies of the crusaders and Estonians. Hill forts, which were the key centres of Estonian countries, were besieged and captured a number of times.

By 1209 Koknese (Kokenhusen) had been taken over by the Order, whereupon Albert of Riga ordered the construction of a Gothic stone castle where the Daugava and Pērse Rivers meet to replace the wooden fortification of the Latvians; the sovereignty of Polotsk was finally revoked in 1215. A truce between the war-weary sides was established for three years (1213–1215). It proved generally more favourable to the Germans, who consolidated their political position, while the Estonians were unable to develop their system of loose alliances into a centralised state. They were led by Lembitu of Lehola, the elder of Sackalia, whose name had come to the attention of German chroniclers as a notable Estonian elder and the central figure of the Estonian resistance by 1211. The Livonian leader Caupo was killed in the Battle of St. Matthew's Day near Viljandi (Fellin) on September 21, 1217, but the battle was a crushing defeat for the Estonians, whose leader Lembitu was also killed.

Dannebrog falling from the sky during the Battle of Lyndanisse, 1219.

The Order established their headquarters at Fellin (Viljandi) in Sackalia, where the walls of the Master's castle are still standing. Other strongholds included Wenden (Cēsis), Segewold (Sigulda), and Ascheraden (Aizkraukle). The commanders of Fellin, Goldingen (Kuldīga), Marienburg (Alūksne), Reval (Tallinn), and the bailiff of Weißenstein (Paide), belonged to the five-member entourage of the Order's Master.

The Christian kingdoms of Denmark and Sweden were also eager for expansion on the eastern shores of the Baltic. In 1218 Albert asked King Valdemar II of Denmark for assistance, but Valdemar instead arranged a deal with the Order. The king was victorious in the Battle of Lyndanisse in Revelia in 1219, in which the origin of the Dannebrog is attributed. He subsequently founded the fortress Castrum Danorum, which was unsuccessfully besieged by the Estonians in 1220 and 1223. King John I of Sweden tried to establish a Swedish presence in the province of Wiek, but the Swedish troops were defeated by the Oeselians in the Battle of Lihula in 1220. Revelia, Harrien, and Vironia, the whole of northern Estonia, fell to Danish control.

Scandinavia in 1219. The realms of Denmark, Norway, Sweden and the Livonian Order. In yellow, the island of Saaremaa (Ösel) claimed by Denmark (conquered by the Livonian Order in 1227) and the territories conquered by Denmark in northern Germany.

In 1223, the Novgorod Republic sent Vyachko to defend the Ugaunian fortress of Tharbata (Yuryev, Dorpat) against the Order. Although his druzhina was small, Vyachko managed to install himself in the fortress with support from local Estonians and to launch several raids against the crusaders. Early in 1224 Emperor Frederick II announced at Catania that Livonia, Prussia with Sambia and a number of neighboring provinces were reichsfrei, that is, subordinate directly to the Roman Catholic Church and the Holy Roman Empire only, as opposed to being under the jurisdiction of local rulers. In response, Albert of Riga besieged Tharbata in 1224 with a large force and offered a peace settlement. Vyachko refused to surrender, however, choosing to die with all of his supporters when the Livonian Order stormed the fortress. At the end of 1224 Pope Honorius III announced to all Christendom the appointment of Bishop William of Modena as papal legate for Livonia, Prussia, and other countries.

Monastic State of the Teutonic Knights, 1225-50.

The Chronicle of Henry of Livonia, one of the greatest medieval narratives, was written probably as a report for William of Modena, giving him the history of the Church in Livonia up to his time. It relates how in 1226, in the stronghold Tarwanpe, William of Modena successfully mediated a peace between the Germans, the Danes and the Vironians. The last Estonian eldership to hold out against the invaders was the island country of Saaremaa (Ösel), whose war fleets had raided Denmark and Sweden during the years of fighting against the German crusaders. A 20,000 strong army under William of Modena crossed the frozen sea while the Saaremaa fleet was icebound, in January 1227, and the Livonian Order conquered the last indigenous stronghold on the island.

After the conquest, all remaining local pagans of Estonia were ostensibly Christianized. William of Modena divided the conquered territory into the Livonian Confederation to appease the bickering Livonian Order and bishops. Denmark controlled the northern part of the country, henceforth known as Danish Estonia. Following the defeat of the Estonians, the crusade moved against the Curonians and Semigallians, Latvian tribes living to the south and west of the Daugava river.

Livonia, ca. 1260.

• Battle of Saaremaa, 1206
• Battle of Otepää, 1208
• Battle of Otepää, 1210
• Battle of the Ümera River, 1210
• Battle of Turaida, 1211
• Battle of Viljandi, 1211
• Battle of Lehola, 1215
• Battle of Riga, 1215
• Battle of Soontagan, 1215
• Battle of Otepää, 1217
• Battle of Soontagan, 1217
• Battle of St. Matthew's Day, 1217
• Battle of Lyndanisse, 1219
• Battle of Lihula, 1220
• Siege of Tallinn, 1221
• Battle of Soela, 1223
• Battle of the Ümera River Bridge, 1223
• Battle of Viljandi, 1223
• Siege of Tallinn, 1223
• Battle of Tharbata, 1224
• Battle of Muhu, 1227

• Chronicle of Henry of Livonia
• Ikšķile

• Eestlased (Estonian)
• Saaremaa 1100 - 1227