The disclosed method for creating credential vaults that use multi-factor authentication to automatically authenticate users to online services may include (1) detecting a user account for an online service that uses multi-factor authentication comprising a token that generates a cryptographic authentication code, (2) creating a virtual representation of the token that is capable of generating the cryptographic authentication code, (3) storing the virtual representation of the token and a set of credentials for the user account in a credential vault for a user, (4) sending a message to the online service that associates the virtual representation of the token with the user account, (5) authenticating the user to the credential vault, and (6) automating the multi-factor authentication process for the online service by providing the cryptographic authentication code and the set of credentials to the online service. Various other methods, systems, and computer-readable media are also disclosed.