diff --git a/otava/bigquery.py b/otava/bigquery.py
index c9b77a67..cf5fafdb 100644
--- a/otava/bigquery.py
+++ b/otava/bigquery.py
@@ -28,6 +28,8 @@
 
 @dataclass
 class BigQueryConfig:
+    NAME = "bigquery"
+
     project_id: str
     dataset: str
     credentials: str
diff --git a/otava/config.py b/otava/config.py
index c0e8d54f..345dedef 100644
--- a/otava/config.py
+++ b/otava/config.py
@@ -127,13 +127,26 @@ class NestedYAMLConfigFileParser(configargparse.ConfigFileParser):
     Recasts values from YAML inferred types to strings as expected for CLI arguments.
     """
 
+    CLI_CONFIG_SECTIONS = [
+        GraphiteConfig.NAME,
+        GrafanaConfig.NAME,
+        SlackConfig.NAME,
+        PostgresConfig.NAME,
+        BigQueryConfig.NAME,
+    ]
+
     def parse(self, stream):
         yaml = YAML(typ="safe")
         config_data = yaml.load(stream)
         if config_data is None:
             return {}
+
         flattened_dict = {}
-        self._flatten_dict(config_data, flattened_dict)
+        for key, value in config_data.items():
+            if key in self.CLI_CONFIG_SECTIONS:
+                # Flatten only the config sections that correspond to CLI arguments
+                self._flatten_dict(value, flattened_dict, f"{key}-")
+            # Ignore other sections like 'templates' and 'tests' - they shouldn't become CLI arguments
         return flattened_dict
 
     def _flatten_dict(self, nested_dict, flattened_dict, prefix=''):
diff --git a/otava/grafana.py b/otava/grafana.py
index bc90998e..b853f3a4 100644
--- a/otava/grafana.py
+++ b/otava/grafana.py
@@ -26,6 +26,8 @@
 
 @dataclass
 class GrafanaConfig:
+    NAME = "grafana"
+
     url: str
     user: str
     password: str
diff --git a/otava/graphite.py b/otava/graphite.py
index 7c3709da..69a7592e 100644
--- a/otava/graphite.py
+++ b/otava/graphite.py
@@ -29,6 +29,8 @@
 
 @dataclass
 class GraphiteConfig:
+    NAME = "graphite"
+
     url: str
 
     @staticmethod
diff --git a/otava/main.py b/otava/main.py
index 60d6e37a..1c2e1e46 100644
--- a/otava/main.py
+++ b/otava/main.py
@@ -518,6 +518,7 @@ def create_otava_cli_parser() -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(
         description="Hunts performance regressions in Fallout results",
         parents=[config.create_config_parser()],
+        config_file_parser_class=config.NestedYAMLConfigFileParser,
         allow_abbrev=False,  # required for correct parsing of nested values from config file
     )
 
diff --git a/otava/postgres.py b/otava/postgres.py
index d014bb6a..7a2aaa03 100644
--- a/otava/postgres.py
+++ b/otava/postgres.py
@@ -27,6 +27,8 @@
 
 @dataclass
 class PostgresConfig:
+    NAME = "postgres"
+
     hostname: str
     port: int
     username: str
diff --git a/otava/slack.py b/otava/slack.py
index 0d9b7511..a0d4bc3d 100644
--- a/otava/slack.py
+++ b/otava/slack.py
@@ -34,6 +34,8 @@ class NotificationError(Exception):
 
 @dataclass
 class SlackConfig:
+    NAME = "slack"
+
     bot_token: str
 
     @staticmethod
diff --git a/tests/config_test.py b/tests/config_test.py
index f1e4a1b1..5ce500eb 100644
--- a/tests/config_test.py
+++ b/tests/config_test.py
@@ -15,10 +15,11 @@
 # specific language governing permissions and limitations
 # under the License.
 import os
+from io import StringIO
 
 import pytest
 
-from otava.config import load_config_from_file
+from otava.config import NestedYAMLConfigFileParser, load_config_from_file
 from otava.test_config import CsvTestConfig, GraphiteTestConfig, HistoStatTestConfig
 
 
@@ -133,3 +134,78 @@ def test_configuration_substitutions(config_property):
         assert accessor(config) == cli_config_value
     finally:
         os.environ.pop(config_property[2])
+
+
+def test_config_section_yaml_parser_flattens_only_config_sections():
+    """Test that NestedYAMLConfigFileParser only flattens the specified config sections."""
+
+    parser = NestedYAMLConfigFileParser()
+    test_yaml = """
+graphite:
+  url: http://example.com
+  timeout: 30
+slack:
+  bot_token: test-token
+  channel: "#alerts"
+postgres:
+  hostname: localhost
+  port: 5432
+templates:
+    aggregate_mem:
+      type: postgres
+      time_column: commit_ts
+      attributes: [experiment_id, config_id, commit]
+      metrics:
+        process_cumulative_rate_mean:
+          direction: 1
+          scale: 1
+        process_cumulative_rate_stderr:
+          direction: -1
+          scale: 1
+        process_cumulative_rate_diff:
+          direction: -1
+          scale: 1
+      query: |
+        SELECT e.commit,
+               e.commit_ts,
+               r.process_cumulative_rate_mean,
+               r.process_cumulative_rate_stderr,
+               r.process_cumulative_rate_diff,
+               r.experiment_id,
+               r.config_id
+        FROM results r
+        INNER JOIN configs c ON r.config_id = c.id
+        INNER JOIN experiments e ON r.experiment_id = e.id
+        WHERE e.exclude_from_analysis = false AND
+              e.branch = 'trunk' AND
+              e.username = 'ci' AND
+              c.store = 'MEM' AND
+              c.cache = true AND
+              c.benchmark = 'aggregate' AND
+              c.instance_type = 'ec2i3.large'
+        ORDER BY e.commit_ts ASC;
+"""
+
+    stream = StringIO(test_yaml)
+    result = parser.parse(stream)
+
+    # Should flatten config sections
+    expected_keys = {
+        'graphite-url', 'graphite-timeout',
+        'slack-bot-token', 'slack-channel',
+        'postgres-hostname', 'postgres-port'
+    }
+
+    assert set(result.keys()) == expected_keys
+    assert result['graphite-url'] == 'http://example.com'
+    assert result['graphite-timeout'] == '30'
+    assert result['slack-bot-token'] == 'test-token'
+    assert result['slack-channel'] == '#alerts'
+    assert result['postgres-hostname'] == 'localhost'
+    assert result['postgres-port'] == '5432'
+
+    # Should NOT contain any keys from ignored sections
+    ignored_sections = {'templates', 'tests', 'test_groups'}
+    for key in result.keys():
+        section = key.split('-')[0]
+        assert section not in ignored_sections, f"Found key '{key}' from ignored section '{section}'"