There are provided systems and methods for code generation and tracking for automatic data synchronization in a data management system. A user associated with an entity, such as an employee of an organization, may purchase an item utilizing a payment instrument or card provided by the organization. In order to provide proper expense allocation, the organization may require receipt matching and storage per use of the payment instrument. An expense management system may provide digital code generation and output on a corresponding physical or digital receipt so that when the receipt is provided to the expense management system, the codes may be matched to backend data stored by the system. The receipts may be processed by extracting text data from an image of a receipt to determine the codes. The codes may then be used to search a database of codes to match to digital transaction data.