In various embodiments, a system and method manages custody and mitigates counterparty credit risk exposure associated with a trade of a financial instrument. A custodian computer system receives an initial margin payment from a pledgor and electronically posts initial margin or collateral payment in a custody account record maintained in the database. A control agreement between the pledgor and a secured party includes agreement details stored in the database. The dual-custody control agreement gives control of the custody account to the pledgor if the secured party defaults on trade obligations, and gives control of the custody account to the secured party if the pledgor defaults on trade obligations based upon default rules. In the event of default, a waiting period is imposed in accordance with the control agreement before the margin payment/collateral is returned to the non-defaulting party and reports are provided to parties involved with the financial transaction.