Trouble with duplicated layers when importing Illustrator file with multiple artboards into InDesign

[Mattia Rosa]

Hi, I have an Illustrator file with multiple artboards and elements arranged on different layers. When I import the file into InDesign, the layers get multiplied based on the number of artboards, and every time I have to go on a treasure hunt to hide the layers that don’t correspond to the graphics on that specific artboard.
I cannot and do not want to split the artboards into separate files.
How can I fix this in Illustrator and InDesign 2025?

[Festive_Elixir4327]

Hi Stabs81.
I've reverted to using an older version 'till the issues are resolved. 

[Ondřej24793640d1mp]

The problem still persists. Please fix it. Thanks.

[Abhishek Rao]

Hi everyone,

Thanks for sharing your updates on this. Could you please confirm the exact versions of Illustrator and InDesign you're currently using? The latest ones are Illustrator 29.8.2 and InDesign 20.5. Are you on these builds? It would also really help if you could share an affected sample file where this duplication happens, so we can test it directly and check with the team.

Looking forward to your update and the file, so we can investigate further.

Abhishek

[Ondřej24793640d1mp]

My programs are up to date, so I’m using the same versions as you mentioned.

The problem is that when I create a new Illustrator file — for example, with 3 artboards and 3 layers — and save it as a .ai file, it shows a total of 9 layers when placed into InDesign.

I noticed that this doesn’t happen when saving the file as a .pdf — in that case, it correctly shows only 3 layers.

This issue didn’t occur in the previous version of Illustrator.

[Abhishek Rao]

Hi @Ondřej24793640d1mp,

Thanks for confirming the versions and sharing your observations. I tested this on my end by creating a new file in Illustrator and placing it into InDesign, and the layers did not duplicate, everything displayed correctly. This makes me think the issue might be specific to the file or something within its structure. Could you please share an affected sample file, so I can test it directly and check with the team if needed?

Looking forward to your update.

Abhishek

[Ondřej24793640d1mp]

Hi, I’m sending the file. It’s a newly created file in Illustrator. When placing it into InDesign (command + D), it shows 9 layers. The file has 3 artboards and 3 layers. In the past, it correctly displayed 3 layers. The issue appeared after the latest update.

[Ondřej24793640d1mp]

TEST.ai

[Ondřej24793640d1mp]

It shows the following error. 

Correct the highlighted errors and try again.

• The attachment's test.ai content type (application/postscript) does not match its file extension and has been removed.

[Kurt Gold]

Abhishek,

as already posted in another thread, here is a very simple Illustrator file for inspection.

https://drive.google.com/file/d/18KXOHa9kYzY7AJ9B294USJ-NmuK_MYiA/view?usp=sharing

It contains 3 artboards and 3 layers. Place it in InDesign while Show Import Options is turned on. In the Import Options dialog go to the Layers tab and see how many layers are listed there.

Do you see 3 layers or 9 layers (duplicates)?

The other thread is here:

https://community.adobe.com/t5/illustrator-discussions/trouble-with-duplicated-layers-when-importing...

[luiz_4122]

I have the same exactly problem.  culd find a solution so far. already downgraded the indesign version. 
on top of that sometimes the Indeseign change the colors of the Illustrator files. or mess with the masks. 

since last update i am having this issue.

[Kurt Gold]

I can also confirm the problem as per the descriptions above (latest versions of InDesign and Illustrator).

Not quite sure if it is an InDesign issue or an Illustrator issue.

By the way, the issue does not occur if you save the Illustrator document to an older format (e.g. Illustrator CC or Illustrator CS6).

[Lea26905664d7vy]

This issue started happening for me exactly as others have described here, and using the current InDesign and Illustrator versions available: Illustrator 29.8.2 and InDesign 20.5. In addition, the InDesign will no longer maintain the layers changed to visible/invisible after using the Object Layer Options. This is very disruptive to workflow. I hope a solution comes soon.

[Abhishek Rao]

Hi @Lea26905664d7vy,

Thanks for sharing your experience and confirming the behavior. We've tried reproducing this issue internally, but haven't been able to so far. To help us investigate further, could you please share an affected sample Illustrator and InDesign file where this duplication and visibility issue occurs? You can upload them to a cloud service like Google Drive or Dropbox and share the link here, or via DM if the files are confidential.

Once we have the files, I'll check them with the product team and update you.

Looking forward to your response.

Abhishek

[Lea26905664d7vy]

Maybe these files will come through? Link to Drive

[Monika Gause]

Can you disable "Save in background" in the preferences, save the file again and see if it's still happening?

https://illustrator.uservoice.com/forums/601447/suggestions/50611952 

[Lea26905664d7vy]

This works!! Thank you for the solution!!

[Abhishek Rao]

Hi everyone,

Thanks so much for sharing your files, observations, and confirmations across different versions. I wanted to let you know that we've logged a bug for this issue where Illustrator files with multiple artboards show duplicated layers when placed into InDesign. The product team is actively investigating it, and a fix is already in progress.

In the meantime, please try the suggested workaround of disabling 'Save in background' in Illustrator Preferences and then saving the file again, this has helped some users avoid the duplication.

I'll keep you all posted here as soon as there’s an update. You can also follow progress on this UserVoice thread: Acrobat layers duplicate excessively in AI file’s compatible PDF – Adobe Illustrator

Appreciate your patience and collaboration while the team works on resolving this.

Abhishek

[Estuardo Ramos]

Linked Illustrator files sometimes show duplicated or missing elements in Photoshop or InDesign, particularly when the objects are grouped.

And you have to go back and ungroup objects so they are not shown duplicated, or with some objects you have to move them, then put it back on place so they show up again.

This is so frustrating because it was never an issue before, and now I can’t rely on my linked files at all. We constantly create mockups in Photoshop and InDesign using linked Illustrator objects, and grouped elements are suddenly duplicating or disappearing. It’s seriously affecting our workflow.

I am using Illustrator for Mac, 29.8.2

Please fix this. 

[Abhishek Rao]

Hi @Estuardo Ramos,

Sorry to hear about the issue with linked Illustrator files. Could you please confirm your exact macOS version and whether this happens with all linked files or just specific ones? Try saving the Illustrator file as a new copy using Save As, then relink it in Photoshop or InDesign to see if it displays correctly. If possible, please share an affected sample file for testing. If the file is confidential, feel free to send it via DM using a link from Drive, Dropbox, or another cloud service.

Let me know how it goes.

Abhishek

[Estuardo Ramos]

Hi It is happening, with most all files, if I make a change and update, sometimes would do it duplicate, sometimes wont show the objects, in fact, it just happened now, I tried to removed some objects that where shown to be duplicated, then save the file,  and update the document inside the other apps (when it was duplicated), and both PS and ID still showed the objects, where it suppos to be none.

is Mac OS 15.5

I shared the files by DM, 

Thank you,

[Monika Gause]

Can you disable "Save in background" in the Preferences, then save the file again and see if it's still happening?  https://illustrator.uservoice.com/forums/601447/suggestions/50611952

[Estuardo Ramos]

Thank you, it worked (for now).