Not sure, but this sounds like it could be the Oracle Prophecies Trilogy by Catherine Fisher, consisting of The Oracle (2003), The Archon (2004), and The Scarab (2005), with the alternative US titles The Oracle Betrayed, The Sphere of Secrets, The Day of the Scarab.
Extracts from the synopses of the books:
In the distant land of deserts and islands, the servants of the god rule the land, his wishes conveyed through the Oracle and interpreted by the High Priestess. Mirany is the new Bearer, afraid of her perilous duties for the god in the rituals of the Oracle, and fearful of her secret questioning ...Does the god truly exist? The priestess is corrupt and in secret partnership with the General, ruler, since the God-on-Earth, the Archon, has no real power - chosen as a child, his face always masked, never seen by outsiders. Should any national tragedy occur, he is also the sacrifice. When the old Archon dies, his spirit migrates into a child, and there are several candidates for succession. But Mirany begins to experience the real visions of the god, discovers which child is the rightful heir, and that the General and High Priestess intend to choose another child and seize power. With only a tomb-robbing scribe and a mad musician for allies, Mirany begins her quest - knowing that, if she is betrayed, her fate will be to be walled up alive in the Archon's tomb ...
the Archon must face a journey of treachery and adventure across the pitiless desert in a bid to save his people ...The Archon vows to lead a pilgrimage to the Well of Songs to seek peace with the Rain Queen and save the land from the terrible drought. The Well is hidden in the mountains across the desert. But he is not the only one with his sight set on the mountains: Argelin, the tyrannical and power-hungry General, follows behind, an ever-present threat, with his heart set on the riches to be found. With only Oblek, Seth and two tomb-thieves known as the Jackal and the Fox for company, the Archon's journey is treacherous and dangerous. They must face the Great Desolation and the monstrous animals outlined on the desert floor, animals with mythical powers, and they must survive without Mirany, bearer-of-the-god and true friend of the Archon, who has had to remain behind to face a threat much closer to home ...
We are again in the distand land of deserts and islands ruled by one god whose wishes are conveyed through the Oracle. The Archon, child god-on-earth, returns from his journey across the desert to the Well of Songs, to find the tyrannical General Argelin has siezed control and his reign of madness is oppressing the Two Lands.