The first land flag was square in shape, with a white cross on a blue background. The marine flags resembled the current national flag more closely, the only difference for merchant marine flags being the reversal of colors in the corner containing the cross. The flag of the merchant ships was eventually merged with that of the navy in 1828, as a recognition for their participation in the Greek War of Independence.

The national flag has been modified several times without being radically altered, mostly as a result of regime changes. In 1833, the Bavarian coat of arms was added to the flags of the army and the navy, and remained until the overthrow of King Otto in October of 1862. With the arrival of King George I in 1863, the crown was introduced into the flags and remained there until the regime change in 1924.