Answer has to do with Abigail
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Goody Proctor never tells us why she does not attend church. In fact, the question is asked of John, not Elizabeth. John says they did not attend church because his wife had been ill, and that their third child had not been baptized because they did not want Parris to do the baptizing. If Elizabeth did not attend church because of Abigail's relationship to John, she does not verbalize her reason.