I went through this same problem a while back. The hard part was the direct deposit, most companies didn't offer it. I finally ended up using http://www.achdi

I went through this same problem a while back. The hard part was the direct deposit, most companies didn't offer it. I finally ended up using http://www.achdirect.com/ http://www.achdirect.com/ I'm not sure I would recommend them - their support was horrible, and the dinged me with a $100 "hidden fee" - but they were the only company I found who had an API for both billing and direct deposit and it did end up working eventually. BrainTree rejected my app too. I wrote a ruby active_merchant plugin to interface with ACHDirect - ping me if you want the source.