diff --git a/.coveragerc b/.coveragerc
deleted file mode 100644
index 9a0c535dcf5..00000000000
--- a/.coveragerc
+++ /dev/null
@@ -1,5 +0,0 @@
-[run]
-omit =
-    */tests/*
-    */_version.py
-    *pygmt/__init__.py
diff --git a/Makefile b/Makefile
index 9f5fdd40e6b..54fa7d9dccd 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 # Build, package, test, and clean
 PROJECT=pygmt
 TESTDIR=tmp-test-dir-with-unique-name
-PYTEST_ARGS=--cov=$(PROJECT) --cov-config=../.coveragerc \
+PYTEST_ARGS=--cov=$(PROJECT) --cov-config=../pyproject.toml \
 			--cov-report=term-missing --cov-report=xml --cov-report=html \
 			--doctest-modules -v --mpl --mpl-results-path=results \
 			--pyargs ${PYTEST_EXTRA}
diff --git a/environment.yml b/environment.yml
index 4a8e69abf92..fec3dbaaebf 100644
--- a/environment.yml
+++ b/environment.yml
@@ -17,7 +17,7 @@ dependencies:
     - pytest
     - pytest-cov
     - pytest-mpl
-    - coverage
+    - coverage[toml]
     - black
     - blackdoc
     - pylint
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000000..334fb0a9922
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,2 @@
+[tool.coverage.run]
+omit = ["*/tests/*", "*/_version.py", "*pygmt/__init__.py"]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index f6a53ef0310..fc05772b072 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -5,7 +5,7 @@ jupyter
 pytest
 pytest-cov
 pytest-mpl
-coverage
+coverage[toml]
 black
 blackdoc
 pylint