The /tʃ/ in the word "nature" is the result of palatalization (see this question). If I understand it correctly, the /t/ (nat) and and /j/ (ure) fused and produced /tʃ/. The letter U had the pronunciation /ju:/ (which is where the /j/ came from). So by palatalization, the pronunciation should be /ˈneɪ.tʃu:r/ (the vowel should not be affected) but now "nature" is /ˈneɪ.tʃər/ and the vowel has changed.

I searched the word's etymology in Wikitionary and according to that entry, "nature" is from Middle English nature and gives the pronunciation /naːˈtiu̯r/ and the entry also says Middle English natur: pronunciation /natuːr/, [naˈtˢuɐ̯ˀ] (I don't understand this square bracket transcription).

As seen, there is /u:/ in the pronunciation of "nature" but nowadays its pronunciation has /ə/ (UK) and /ɚ/ (US). There are many other words that end with "ture" and show the same change but I think this one is enough to demonstrate the change.

Was there a change from /u:/ to /ə/ (or /ɚ/) in the history of English?

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    It's not specific to /u:/: many unstressed vowels are "reduced" (mostly, centred) in English, though there is variation between dialects and even between individual words. See Wikipedia – Colin Fine Nov 3 '20 at 12:24
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    It's not the "t" before it that changed the pronunciation of the /u/ but the "r" after it. Compure closure, figure, seizure. – Peter Shor Nov 3 '20 at 15:06
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    "[naˈtˢuɐ̯ˀ]" is the transcription for natur in Danish, not for any form of English. – herisson Nov 3 '20 at 17:24

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