Finally, I've found a solution to my problem.
I created the workspace with the projects inside without any source control options. Then, I manually created a single git repo inside my source folder by doing the following in the Terminal.
cd /path-to-my-source-code/.git
git init
git add .
After, I added a .gitignore file inside the .git folder as suggested in https://stackoverflow.com/a/12021580/209824.
The final step was to restart Xcode.