As a part of his missionary work, he learned Persian and strove to genuinely understand Islam, particularly Shi'a Islam, Persia and Persian culture. During his missionary work in Persia, he also encountered the Bahá'ís, a large religious minority there. Much of his ministerial work involved developing Christian apologetic responses to these religions.
With respect to the Bahá'í Faith, his 1931, Baha'ism, Its Origin, History and Teachings was the first of two books, and several apologetics articles on the subject. Along with Earl E. Elder he translated Bahá'u'lláh's Kitáb-i-Aqdas, one of the central books of the religion; this translation was published by the Royal Asiatic Society in 1961. In 1974, a new follow-up, The Baha'i Faith: Its History and Teachings added additional material not available previously.
This latter book was also critically reviewed by academics. One reviewer noted:
"The title suggests (and this impression is supported by the "blurbs" on the back cover) that we have in our hands a "standard" work on Bahá'ísm ... In fact what we are presented with is an all-out attack on, a merciless tirade against, Bahá'ísm, but treated not, as one might expect from the author's credentials (Presbyterian missionary in Iran for 40-odd years), from the Christian, but from the Azali point of view....Of course Dr. Miller may argue that he and his collaborators have done little more than present facts, from which only certain conclusions can be drawn. But contrary to common belief, the mere accumulation of facts is no guarantee of impartiality."