Is there a way to customise bookmark icons in Chrome?

I don't think there's a built in way of customizing the favicon, but you can use a chrome extension called Bookmark Favicon Changer which will let you modify it.

There isn't currently (November 2019) a way to do this natively, although this functionality is a Chrome feature-request that I would recommend up-voting.

Your options at present are (from easiest to difficult):

• Use an emoji in the bookmark name
• Install a Chrome extension, e.g. Bookmark Favicon Changer or Favicon Changer
• Create a custom HTML redirect on your PC or server as per this article

Q: Is there a way to customise bookmark icons in Chrome?

A: Not easily.

Bookmark icons are stored in an SQLite database in ...
%LocalAppData%\Google\Chrome\User Data\Default\Favicons.

The icon images are stored (in png format) in the "image_data" field in "favicon_bitmaps" table. This table is indexed on the "image_id" field (numeric). The "image_id" value can be found in the "icon_mapping" table via the indexed "page_url" field.

Additional notes:
1. sometimes there's more than one image per "image_id" (ie when there are different sized images - eg 16x16px, 32x32px)
2. the Favicons file can't be updated (by external applications) while Chrome is running.

This website provides a wise way to achieve this also:

"it’s done by creating an HTML file on your PC or on a web server that redirects to your preferred website (by using simple HTML redirects)."

http://www.minterest.com/how-to-change-chrome-bookmark-icon/

(In fact, that's likely what the "Bookmark Favicon Changer" performs behind the scene, as it requires to enable the option "allow access to file URLs", which also means that the solution does not follow your profile on each PC you log in with Chrome).