Have you the CSS snippet option turned on ? Or do you have the css file on the right folder ?
Like @odulhin mentioned, you might have forgotten the CSS snippet.
Alternatively, just on the off chance you or someone else runs into the same niche issue as I did: if you “Add a new note from annotations” in Zotero, the imported annotations won’t show up in call-out boxes at all. They’ll just look like plain text. The Zotero Integration and this template draw from the annotations themselves, so if you’ve got an Annotations note attached to the ref you’re trying to import, you can probably delete it.
If you do that and then find that no annotations are imported at all, check how many PDFs you have attached to the reference in Zotero. As far as I can tell this template only draws annotations from the top one, so delete any duplicate PDFs until your annotated PDF is the only one remaining. Those two steps fixed it for me.
I would be interested in seeing a template that could pull annotations from multiple PDFs, since having duplicates appears to be a relatively common problem for me.
Thank you for this example, it looks so great!
However I have found that when I imported a item from Zotero, the highlights are ordered by their orders of appearance, instead of grouped by their highlights. I am not familiar with the coding part, so any idea would help! Thank you very much.
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Hi to be honest with I struggled quite a bit to write my template but I found a post which seems to answer your question Zotero Integration – Import Templates? - #133 by jujumartini
Hi, thanks you very much for the template. I have a question : is there a way to change the color of the highlight ? I find it very bright and i wanted to get the citation without it.
thanks for your help!
Thanks to everyone on this thread who has been so generous with their templates/responses. As a complete Obsidian newby, with limited scripting skills (very limited), this has all been extremely helpful.
@nocona I have managed to implement your template, and in doing so have a) learnt a fair bit about obsidian, and b) found a solution that suits my use case and level of skill. Thanks again.
How can I activate the CSS snippet? Can someone help?
My final template with Tags imports included. thanks to @Albialy
---
year: {{date | format ("YYYY")}}
tags: research, {{allTags}}
authors: {{authors}}
Abstract: {{abstractNote}}
---
### {{title}}
{{pdfZoteroLink}}
### Notes
{% for annotation in annotations -%}{%- if annotation.annotatedText -%}{% if 'Red' in annotation.colorCategory %}
##### {{annotation.annotatedText | escape }}{% else %}
<mark class="customZot-{% if annotation.color %}{{annotation.colorCategory}} {% endif %}">{{annotation.annotatedText | escape }}</mark> ([{{annotation.page}}](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.page}}&annotation={{annotation.id}}))
{% endif %}{%- endif %} {% if annotation.imageRelativePath %} ![[{{annotation.imageRelativePath}}]]{% endif %}{% if annotation.comment %}
>{{annotation.comment}}
{% endif %}{% endfor -%}
Hello, please could you help me! I’ve been trying to use this template and thought I’d set it up correctly but for some reason when I import a paper from Zotero using the template only the annotations are imported but none of the tabs or bibliographical information. Could you advise where I am going wrong? Thanks in advance!!!
Just wanted to say thank you for this. It works really well for my workflow.
Hi, thanks for this really useful template. I’m having trouble with the bibliography: it keeps appearing two lines below the {{bibliography}} marking. I’ve got zotero integration extension and Zotero export style both set to Nature.
This section of the template looks like:
**Citation**:: {{bibliography}}
but I get, for example
Anyone know a solution to this? Thanks!
Numbered bibliography styles have line breaks in them. You can correct this by replacing line breaks with spaces. This should do the trick (it’s what I do in my template):
{% if bibliography %}**Citation**:: {{bibliography|replace("\n","" )}}{% endif %}
Annotations already have a default URI, I really have no idea why anyone would use the following:
zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.page}}&annotation={{annotation.id}}
This is not only unnecessarily complicated, but it will also fail automatically if sources are not located in “My Library”, e.g., group libraries. Exchange it for the following:
{{annotation.desktopURI}}
How do I import only the surname of an author? I want to title the annotations the following way: Surname Year PageLabel.
{% for annotation in annotations -%}
[!{{AUTHOR-SURNAME}} {{date | format(“YYYY”)}} {{annotation.pageLabel}}|{{annotation.color}}]+
A shortcut would be the citekey. But I actually just want to find out how to only import the surname of the author.
I also want to know how I can import all purple annotations under heading A of the note and all the other annotations under heading B.
Heading A
purple annotation 1
purple annotation 2
purple annotation 3
Heading B
yellow annotation 1
yellow annotation 2
green annotation 1
yellow annotation 3
…
Can anybody help me with this? 
Hi!
I loved your template so so so much, however, I’m just starting with obsidian and I must be making some mistake because your template simply doesn’t work (it’s as if there was no template). I’m attaching some screen caps so that you can tell me what I may be doing wrong? I also wonder if it’s that I need some plugins that I don’t have, but I cannot imagine which?
Thank you so much in advance. 
Natalia
Hello Nocona, very nice template! I’d like to integrate the “notes” and “annotations” part to my template (as the metadata part is already well organized to suit my needs); could you please tell me which part of the code I should use in my template? I guess everything from line 138 (from your GitHub) and maybe line 1-48? Sorry I can hack some code but I’m a total noob… 
Fantastic template. Is there a way to it groups the annotations by colour, instead of having them in sequential non-grouped order?