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I've done a bit of digging, and for the life of me, I cannot find any clear record or explanation for why Japanese ココア is pronounced the way it is.

Sources researched to date:

Lots of information is out there about カカオ and ココア, and what each of them are, and how the former is turned into the latter. I can confirm in various sources that カカオ is borrowed from Spanish, and ココア is borrowed from English. But I can find nothing about why ココア is pronounced as //ko.ko.a//.

My suspicion is that this is the result of "book pronunciation", based on the English spelling cocoa and simply reading it out vowel-for-vowel. A distant alternative possibility is that the Japanese word somehow metathesized the vowels after borrowing cacao, the common term for this in many other European languages, including the Japanese-contact trifecta of Dutch, Spanish, and Portuguese. English wound up with a pronunciation of //ˈkoʊ.koʊ// (US) or //ˈkəʊ.kəʊ// (UK) not through any metathesis, but rather through early confusion with coco (as in coconut), as best I can tell. (See also the Wiktionary entry.) If ココア were borrowed from spoken English, we'd expect something more like //kóꜜò.kòò//, instead of the //kóꜜ.kò.à// and //kó.kóꜜ.à// pronunciations evident in modern usage.

Does anyone have any solid evidence for why we have this unexpected word form? Or any leads on academics or references that discuss this oddity of etymology?

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    I think your first conjecture is the most likely. There's a lot of examples where English words transcribe into Japanese according to how they spell as opposed to how they are pronounced. That explains the ア. Pizza is another example. ピザ. I have also lighted upon this article that basically confirms what you say about the English word cocoa.
    – Eddie Kal
    Commented Dec 6, 2020 at 7:42
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    I've been interested in this fact too, and read Tokugawa's diary where he allegedly drinked ココア. It was a red herring. The original text of that part is written in French. He drinked "chocolat". Commented Dec 6, 2020 at 8:27
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    @EiríkrÚtlendi Translation is by the book's editors. They say that the original French text was written for his language exercise, and corrected by his tutor. Commented Dec 8, 2020 at 0:45
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    @EiríkrÚtlendi Editors of the 1999 book. It's a collection of all sorts of manuscripts during his trip. This journal was written on his notebook unpublished. Commented Dec 8, 2020 at 1:14
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    @jarmanso7, my copy of Daijirin sources JA ボタン from PT botão, where the nasal -ão may well sound like アン to a Japanese ear. Harder to find due to the lemmatization (where the word is filed), but I did just find the KDJ entry, which also points to Portuguese as the source. Commented Apr 20, 2022 at 23:24

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I don't have a conclusive case, but it seems like ココア was considered wrong at some point. If it was an accidental mistake that stuck, there might not be a very logical explanation.

Some old sources say ココア is a mistaken term with warped pronunciation (訛り), maintaining that コーコー is more correct.

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