For no apparent reason, Flask decided to use a folder one level above the actual project directory. Project details: Working directory in Run/Debug is set correctly Python console in PyCharm starts in the correct directory The parent folder is mentioned once -- in the "Paths to .env files" field, where a single .env file is included Settings -> Project: projectname -> Project Structure shows the correct structure (intended working directory is set as project root) Just in case, I set the working directory for both Python and Flask consoles in Settings -> Build, Execution, Deployment -> Console to project root Despite the working directory being set in every place I could think of, when I try to use the project, I get an error because it tried to load a file from the parent directory (e. g. ~/file.yml instead of ~/projectname/file.yml). Running the project manually via the default Python configuration with the same working directory and env file path settings works fine. What am I missing? Continue reading...