diff --git a/airflow-ctl-tests/pyproject.toml b/airflow-ctl-tests/pyproject.toml
index d401975ad73f4..24c7f561ed196 100644
--- a/airflow-ctl-tests/pyproject.toml
+++ b/airflow-ctl-tests/pyproject.toml
@@ -40,8 +40,15 @@ dependencies = [
     "apache-airflow-devel-common",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
+
 norecursedirs = [
     ".eggs",
 ]
diff --git a/airflow-ctl/pyproject.toml b/airflow-ctl/pyproject.toml
index 267ec58b5d7ef..8c2fe12a7c5e0 100644
--- a/airflow-ctl/pyproject.toml
+++ b/airflow-ctl/pyproject.toml
@@ -163,7 +163,7 @@ input = "../airflow-core/src/airflow/api_fastapi/core_api/openapi/v2-rest-api-ge
 output = "src/airflowctl/api/datamodels/generated.py"
 
 ## pytest settings ##
-[tool.pytest.ini_options]
+[tool.pytest]
 addopts = [
     "--tb=short",
     "-rasl",
@@ -196,7 +196,7 @@ testpaths = [
 ]
 asyncio_default_fixture_loop_scope = "function"
 
-pythonpath = "tests"
+pythonpath = ["tests"]
 
 # Keep temporary directories (created by `tmp_path`) for 2 recent runs only failed tests.
 tmp_path_retention_count = "2"
diff --git a/airflow-e2e-tests/pyproject.toml b/airflow-e2e-tests/pyproject.toml
index 8b03df204b185..a9406aa2a6feb 100644
--- a/airflow-e2e-tests/pyproject.toml
+++ b/airflow-e2e-tests/pyproject.toml
@@ -41,8 +41,15 @@ dependencies = [
     "boto3>=1.37.2",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
+
 norecursedirs = [
     ".eggs",
 ]
diff --git a/clients/python/pyproject.toml b/clients/python/pyproject.toml
index a7a228116413f..59593b1d8dd81 100644
--- a/clients/python/pyproject.toml
+++ b/clients/python/pyproject.toml
@@ -102,9 +102,14 @@ include = [
     "/airflow_client",
 ]
 
-[tool.pytest.ini_options]
+[tool.pytest]
 # make sure that pytest.ini is not read from pyproject.toml in paraent directories
-addopts = "--color=yes --cov-config=pyproject.toml --cov=airflow_client"
+addopts = [
+    "--color=yes",
+    "--cov-config=pyproject.toml",
+    "--cov=airflow_client",
+]
+
 norecursedirs = [
 ]
 log_level = "INFO"
diff --git a/dev/breeze/pyproject.toml b/dev/breeze/pyproject.toml
index 7a08ada848871..9e87dd5399db5 100644
--- a/dev/breeze/pyproject.toml
+++ b/dev/breeze/pyproject.toml
@@ -89,8 +89,15 @@ name = "airflow_breeze"
 line-length = 110
 target-version = ['py310', 'py311', 'py312']
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
+
 norecursedirs = [
     ".eggs",
 ]
diff --git a/docker-tests/pyproject.toml b/docker-tests/pyproject.toml
index 25c20506506bc..fe2ced2cb369d 100644
--- a/docker-tests/pyproject.toml
+++ b/docker-tests/pyproject.toml
@@ -39,8 +39,14 @@ dependencies = [
     "apache-airflow-devel-common",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
 norecursedirs = [
     ".eggs",
 ]
diff --git a/helm-tests/pyproject.toml b/helm-tests/pyproject.toml
index 03d047f388dfa..799fc4cebb70f 100644
--- a/helm-tests/pyproject.toml
+++ b/helm-tests/pyproject.toml
@@ -39,8 +39,14 @@ dependencies = [
     "apache-airflow-providers-cncf-kubernetes",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
 norecursedirs = [
     ".eggs",
 ]
diff --git a/kubernetes-tests/pyproject.toml b/kubernetes-tests/pyproject.toml
index 2ccb1824be15d..bced4f3384ddc 100644
--- a/kubernetes-tests/pyproject.toml
+++ b/kubernetes-tests/pyproject.toml
@@ -43,8 +43,14 @@ dependencies = [
     "requests>=2.32.0,<3",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
 norecursedirs = [
     ".eggs",
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 674a8d12fce8a..8682a8544c9f0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -906,7 +906,7 @@ mark-parentheses = false
 fixture-parentheses = false
 
 ## pytest settings ##
-[tool.pytest.ini_options]
+[tool.pytest]
 addopts = [
     "--tb=short",
     "-rasl",
diff --git a/task-sdk-integration-tests/pyproject.toml b/task-sdk-integration-tests/pyproject.toml
index 86fdb7922654c..100ed5ee9ddb0 100644
--- a/task-sdk-integration-tests/pyproject.toml
+++ b/task-sdk-integration-tests/pyproject.toml
@@ -40,8 +40,14 @@ dependencies = [
     "apache-airflow-devel-common",
 ]
 
-[tool.pytest.ini_options]
-addopts = "-rasl --verbosity=2 -p no:flaky -p no:nose -p no:legacypath"
+[tool.pytest]
+addopts = [
+    "-rasl",
+    "--verbosity=2",
+    "-p", "no:flaky",
+    "-p", "no:nose",
+    "-p", "no:legacypath",
+]
 norecursedirs = [
     ".eggs",
 ]
diff --git a/task-sdk/pyproject.toml b/task-sdk/pyproject.toml
index 4a83e9c328784..2ba2764acdf24 100644
--- a/task-sdk/pyproject.toml
+++ b/task-sdk/pyproject.toml
@@ -205,7 +205,7 @@ url = 'http://0.0.0.0:8080/execution/openapi.json'
 output = 'src/airflow/sdk/api/datamodels/_generated.py'
 
 ## pytest settings ##
-[tool.pytest.ini_options]
+[tool.pytest]
 addopts = [
     "--tb=short",
     "-rasl",
@@ -236,7 +236,7 @@ testpaths = [
 ]
 asyncio_default_fixture_loop_scope = "function"
 
-pythonpath = "tests"
+pythonpath = ["tests"]
 
 # Keep temporary directories (created by `tmp_path`) for 2 recent runs only failed tests.
 tmp_path_retention_count = "2"