If I file for Chapter 13 Bankruptcy, will the trustee take over control of my checking account?

Don't worry.  In bankruptcy, neither the trustee nor anyone else will be seizing your bank account. You can use your bank accounts as usual, as well as your other property. In some circumstances, an item of "non-exempt" property may be taken but this is something that you should know about in advance of filing for bankruptcy. I wouldn't worry about it unless your lawyer tells you that it could be a concern in which case you have to weigh your options. 

Carol O'Connor Cadiz
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Attorney & Owner at O'Connor Cadiz Law: Bankruptcy, Injury, Real Estate & Mediation