Pentru a îmbunătăţi organizarea apărării în Anatolia, Heraclie a introdus conceptul de ''theme'' (''themata''), un serviciu militar bazat pe subvenţii ereditare de terenuri pentru diviziile de soldaţi. Acestea erau guvernate sub administraţie militară în fiecare themă, comandată de un guvernator militar (''strategos'').
In the 630s, the Arab tribes, unified under Muhammad, became a formidable force that attacked Syria and Palestine. Heraclius had to depend upon his generals for the defense against these attacks as he had become ill after his triumph over the Persians and could not personally lead his army. In this his generals failed him. Palestine and Syria were attacked in 634. In 636 , the larger Roman force was crushed in the Battle of Yarmuk, and by 639 Syria and Palestine were lost. At the time of his death, most of Egypt was under the control of the Muslim Arabs.
Heraclius died in Constantinople on [[ February 11]] , 641. He was succeeded by his sons Constantine III and Heraklonas.