Don't prompt for opening certain external apps in Chrome
So I think you are referring to protocol handlers - this is the message that says &quot;Are you sure you want to open this link in ?&quot;
If so, try this:

Quit Google Chrome.
With Finder selected, hit the Shift-⌘-G and enter
the folder address ~/Library/Application Support/Google/Chrome.
Open the &quot;Default&quot; folder, and open the &quot;Preferences&quot; file in a text
editor like Text Editor.
Search for the phrase “excluded_schemes,”
which houses your list of protocol handler preferences in the text
file.
Search for the protocol (like “itmss” for iTunes, or
“slack” for Slack) and change its state from “false” to “true,”
taking care not to remove any punctuation.
Save the file, and re-open
Chrome.

** This only works if you've previously left &quot;Always use this app for this filetype&quot; unchecked, and may not work for all versions of Chrome  ***