This question might get closed as being too subjective - for any particular book, it depends on what the author chose to include in the Appendix and what your own preference is.
OTOH, by definition, an Appendix is supplementary , so the general rule would be to read any Appendix after
you've read the book.
A couple of exceptions: If the author clearly says something like "read Appendix 1 between Sections 2 and 3 of the novel."
If the Appendix is just a glossary, you'd to it if you forget a specific word,
e.g. (I can't think of a good Dune example, so here's one from "The Chronicles of Thomas Covenant") the difference between lomillialor and lor-liarill.
For Dune (and for LotR, which also has substantial Appendices), I'd definitely read the Appendix after
- there's nothing in there you need to know to enjoy the book.
scifi.stackexchange.com/users/4167/Ward - Reinstate Monica
The only appendices I've encountered (Trudi Canavan's Magicians trilogy) have contained glossaries of the fantasy language (not something you see in non-speculative fiction) she has created which helped to explain a lot of things whilst I was reading.
Once I learned it was there
I read it through, but
I kept turning back to it.
There were no spoilers there, and I can't think of any appendix that would contain a spoiler.
That would probably be in an epilogue of similar.
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One of the appendices of Dune would be a pretty big spoiler, as it was apparently written to address a pretty severe plot hole, so I'd save them for after.
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Some books like House of Leaves have appendacies that are meant to be read at a specific time during the reading if the main book and the story isn't complete without it.
I would suggest that you read the appendacies when needed.
Like if there's a footnote that references them or if you're confused about an element in the book and you know it's addressed in the appendix.
In some cases though, the appendix is completely optional and is just there for hardcore fans.
Examples are some of the Lord Of The Rings appendacies that go over the different languages.
I doubt that you NEED to read them to enjoy the story, but they are there to make the universe more complete.
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There is a good reason that the appendix is at the end of the novel and that's because it will often "spoil" major plot elements within the book or may even completely redefine the tone of the book.
A perfect example of this would be the " Principles of NewSpeak " appendix at the end of the book "1984" by George Orwell which places the entire book (e.g. that you've just read) into a historical context of having been written approximately 50 years prior to the defeat of Big Brother.
In specific relation to Dune, of the four appendices , the one labelled " A Report on Bene Gesserit Motives and Purposes " is probably the most spoilerish and should definitely not be read before the novel.
The glossary has no major spoilers and may help your general understanding, however it's largely unnecessary since most of the major terms are extensively explained in the book itself.
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It's at the end, there's (generally) no indication in a novel that it is back there, and it tends to be optional material, so read it last.
I'd be worried about spoilers too when it comes to arbitrary appendices.
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I'm about 100 pages into  Dune . I noticed the novel has more than one appendix.  As a rule of thumb, when a sci-fi or fantasy novel has an appendix, should I:    read through it before I start the book;  reference it occasionally while reading the book;  or bask in its glory after I've read the book?   My main concern is running into some kind of spoiler back there!  What do you think?  Edit:  Dune has some  major  spoilers in its appendices!
In general, should I look through a novel's appendix(es) before, during or after reading?
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It is doubtful that you NEED to read the appendices to enjoy the story, but they are there to make the universe more complete.  For Dune (and for LotR, which also has substantial appendices), some people recommend reading the Appendices  after  the book. Others suggest reading the appendices when needed. The appendices are at the end of books because they may "spoil" major plot elements. It is, for the most part, suggested that the appendices be read at the end.
It is, for the most part, suggested that the appendices be read at the end.