cargo-deep-clean.sh

find . | grep "Cargo.toml$" |                     # Find all cargo.toml files \
sed 's#/[^/]*$##' |                               # Remove the filename leaving us with the directories containing cargo.toml files \
xargs -L1 printf "cd \"%s\"; cargo clean; cd -\n" |   # Print "cd path/to/crate; cargo clean; cd -" \ 
bash                                              # Execute

Aternative without needing a script

find ~/Documents/projects -name Cargo.toml -type f -prune -exec echo "In {}" \; -exec cargo clean --manifest-path {} \;