diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..a12cb5f
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,13 @@
+[run]
+branch = True
+source = cellxgene_gateway
+
+[report]
+exclude_lines =
+    if self.debug:
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True
+omit =
+    tests/*
\ No newline at end of file
diff --git a/.github/workflows/pr-checks.yaml b/.github/workflows/pr-checks.yaml
index 9b68582..68539ce 100644
--- a/.github/workflows/pr-checks.yaml
+++ b/.github/workflows/pr-checks.yaml
@@ -45,5 +45,16 @@ jobs:
         run: |
           eval "$(conda shell.bash hook)"
           conda activate cellxgene-gateway
-          python -m unittest discover tests
-          bash <(curl -s https://codecov.io/bash)
+          coverage run -m unittest discover tests
+
+      - name: Check coverage
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          coverage report --fail-under 41
+          coverage xml -i
+
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v1
+        with:
+          fail_ci_if_error: true
diff --git a/.gitignore b/.gitignore
index 4f3c841..1e16908 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,6 +55,7 @@ htmlcov/
 .nox/
 .coverage
 .coverage.*
+htmlcov
 .cache
 nosetests.xml
 coverage.xml
diff --git a/README.md b/README.md
index 58d6981..ab79351 100644
--- a/README.md
+++ b/README.md
@@ -140,6 +140,12 @@ pre-commit install
     python -m unittest discover tests
 ```
 
+## Code Coverage
+```bash
+    coverage run -m unittest discover tests
+    coverage html
+```
+
 ## Running Linters
 
 pip install isort flake8 black
diff --git a/environment.yml b/environment.yml
index 51db748..0282a56 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,7 @@ dependencies:
 - flask
 - psutil
 - black
+- coverage
 - pip
 - pip:
   - flask-api