Iglesia ni Cristo acknowledges that the Comma Johanneum is not found in the earliest Greek manuscripts. The phrase was a later Latin addition inserted to support Trinitarian doctrine. This textual fact supports the church's broader rejection of the Trinity: the doctrine was not present in the apostolic faith but was a later development.

Iglesia ni Cristo uses the textual-critical evidence to support its conviction that the Trinity is an unbiblical doctrine not found in the original apostolic teaching. The absence of the Comma from early manuscripts is one piece of evidence that Trinitarianism is a subsequent theological innovation.