The solution is to define an overrideConfigFile option to point to the location of the ESLint configuration file in the workspace in the settings.json like so:

{
    "eslint.options": { "overrideConfigFile": "./path/to/eslint.config.js" }
}

Since ESLint v8.x, the ESLint extension in VSCode uses the ESLint Class API to "[...] configure how ESLint is started". The extension documents that "[...] to point to a custom .eslintrc.json file using the new ESLint API" is as shown above.

For good measure, since the configuration file used is the new flat config file, the eslint.useFlatConfig setting can also be explicitly set to true. In the settings.json:

{
    "eslint.useFlatConfig": true
}

Since version 3.0.5 of the extension, the activation of this setting works like this:

• 8.57.0 <= ESLint version < 9.x: setting is honored and defaults to false.
• 9.0.0 <= ESLint version < 10.x: settings is honored and defaults to true.

Hi @PaulHaze, the ESLint core team does not maintain the VSCode extension for ESLint. Please contact the maintainers there for more help.

When I have a root directory with multiple projects in, then it only looks for the config in the top level directory that is open, not in the root of the current project I am working on.

That's how the flat config system is designed. ESLint expects your config file to be in the root of the project and once it finds this file it stops searching for eslint.config.js files, unlike how it worked in the eslintrc config system where config files would be merged together. I believe the best way to solve this is to move all your individual ESLint configurations into a single root eslint.config.js and target specific project folders using the files key.

config file resolution doc
vscode-eslint

So I managed to solve this myself,

You need to specify in settings.json where the eslint.json file is. The code is

    "eslint.workingDirectories": [
    "./projectmt/"
] 

This got my linter working in vscode again, hope this helps someone in the future.