Since Cargo 1.56, you can use the configurable-env feature via the [env] section in config.toml. This is not the same file as Cargo.toml, but it can still be set per project:
[env]
FOO = "bar"
PATH_TO_SOME_TOOL = { value = "bin/tool", relative = true }
USERNAME = { value = "test_user", force = true }
Environment variables set in this section will be applied to the environment of any processes executed by Cargo.
relative means the variable represents a path relative to the location of the directory that contains the .cargo/ directory that contains the config.toml file.
force means the variable can override an existing environment variable.
For more information about the history of this feature, see the related GitHub issue.