Usually yeah it will. But if it doesn’t work for you, then you can try specifying absolute path to flake8 and enable it explicitly like so :
"python.linting.flake8Enabled": true,
"python.linting.flake8Path": "path/to/flake8",
you can even specify path to your conda environment :
"python.condaPath": "path/to/condaenv/",