A payment processing system allows partial captures and full deposits after receiving a partial authorization result on a requested card transaction. When the partial amount authorized is less than the full transaction amount, but above a certain value (which can be merchant specified), the system can accept the partial amount (a partial deposit or partial capture) as payment for the transaction. When the partial amount authorized is less than the full transaction amount, and below a certain value (which can be merchant specified), the system can make a full deposit of the transaction amount. The system can use one or more factors, including historical information, in determining whether to attempt a full deposit.