Wheeler announced her "voluntary and amicable" split from the fledgling site on her blog.
She said her departure had nothing to do with her coverage of Ukraine, or the site's relative inactivity that editor-in-chief John Cook addressed last month.
(Cook announced earlier this week that The Intercept is hiring, perhaps a sign that the site is awaking from its temporary slumber.)
Wheeler said her reasons for leaving "predate both of those things, to January."
"I’ll have more to say–not about The Intercept, per se, but about things I’ve learned about my own journalism over the last 7 months, as the Edward Snowden story played out and the Intercept discussed hiring me–at some later point, after some reflection," she wrote.
Wheeler contributed one story to The Intercept that was published in March.