The disclosed computer-implemented method for utilizing custom tagging to protect against phishing attacks from malicious applications may include (1) associating a tag with a source application such that the tag is displayed in a user interface generated by the source application (2) launching a target application sharing at least one common feature with the source application, (3) determining, upon launching the target application, whether a user interface generated by the target application is an attack by a malicious application potentially causing harm to the computing device based on a presence or absence of the tag in the user interface, and (4) performing a security action with respect to the target application to protect the computing device from the attack when the tag is determined be absent from the user interface generated by the target application. Various other methods, systems, and computer-readable media are also disclosed.