During the First Balkan War, Colonel Zhekov served as chief of staff of the 2nd Army which was tasked with the initial siege and latter the storming of the important [citation needed] fortress of Edirne.

After his experience of the Balkan Wars Tsar Ferdinand refused to take command of the Bulgarian Army as Commander-in-Chief and personally favored Nikola Zhekov for the post, which he assumed on 24 September 1915.

Separately, Zhekov managed in throwing back the Allied offensives on the Salonika front in the autumn of 1916 and the spring of 1917 at the battles of Florina and Lake Prespa.

In the summer of 1918 he became ill and on 8 September was forced to go to Vienna for medical treatment, leaving the command of the army to the deputy commander-in-chief general Georgi Todorov.

It was during this critical time when the Allied Vardar offensive in Macedonia managed to break the Bulgarian lines at Dobro Pole and lead to the Armistice of Salonica.

He returned in 1921 to defend his reputation and was sentenced to ten years imprisonment by Stamboliyski's BANU government but was granted pardon after the 1923 coup d'état and was released in 1924.

During World War II General Zhekov established a friendly relationship with Adolf Hitler and following the defeat of France in 1940 he was invited by the Führer to visit Paris as his guest.