By the mid-16th century the international situation had worsened for Old Livonia. The territory was divided into small feudal states whereas the neighbouring territories had evolved into states with strong central power – in the East Russia, in the South the Polish–Lithuanian Commonwealth (Rzeczpospolita) and in the West Sweden and Denmark. The situation was made worse by the secularization of the Order and also the Reformation. The greatest danger rose from the East with tsar Ivan the Terrible.
In 1554 Russia did not agree to extend peace with Livonia when no compliances were made regarding trade. In addition the tsar asked for the paying of the “Tartu tax”, arguing that the territory of Southeastern Estonia had once belonged to Russia. As the tsar’s demands were not met, Ivan the Terrible launched a military campaign against Livonia. The Order was weak and could not provide proper resistance. The last battle of the Order was held at Härgmäe. Local rulers started to look for foreign assistance and protection: the Western part of the counry went to the Danish King Frederik II, Northern Estonia to the Swedish King Erik XIV and Southern Estonia to Poland.
However, Russia was not fooled by the change of landlords and the war continued for the next two decades. Sweden and Poland eventually managed to force the Russians out of Livonia. The Jam Zapolski Peace was concluded between Poland and Russia (1582) and the Pljussa Treaty between Sweden and Russia (1583). As a result Northern Estonia belonged to Sweden, the Island of Saaremaa to Denmark and Southern Estonia to Poland.
After the many conflicts between local powers Sweden under Christina I gained control over the whole of Estonian territory in 1660. The wars between Sweden and Poland can be viewed in the overall context of all-European religious wars: Sweden was a protestant state and Poland a catholic country.
Estonians took part in all of those conflicts as they fought in the armies of all the opposing countries. Some of them even reached officer rank. To local people wars were devastating: Estonia lost more than half of its population with the Livonian and the following smaller wars.