diff --git a/README.md b/README.md
index 89264f7eb..e34278866 100644
--- a/README.md
+++ b/README.md
@@ -351,15 +351,16 @@ and YAML. Load the file with the `--config-file` flag:
 ./cloud-sql-proxy --config-file /path/to/config.[toml|json|yaml]
 ```
 
-The configuration file format supports all flags, in lowercase and with an
-underscore instead of a hyphen.
-
-For example:
+The configuration file format supports all flags. The key names should match
+the flag names. For example:
 
 ``` toml
-instance_connection_name = "proj:region:inst"
-auto_iam_authn = true
+# use instance-connection-name-0, instance-connection-name-1, etc.
+# for multiple instances
+instance-connection-name = "proj:region:inst"
+auto-iam-authn = true
 debug = true
+debug-logs = true
 ```
 
 Run `./cloud-sql-proxy --help` for more details.
diff --git a/cmd/config_test.go b/cmd/config_test.go
index 62ca0b8da..8b252dff5 100644
--- a/cmd/config_test.go
+++ b/cmd/config_test.go
@@ -30,41 +30,44 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 		desc   string
 		args   []string
 		setup  func()
-		assert func(t *testing.T, command *Command)
+		assert func(t *testing.T, c *Command)
 	}{
 		{
 			desc:  "toml config file",
-			args:  []string{"--config-file", "testdata/config.toml"},
+			args:  []string{"--config-file", "testdata/config-toml.toml"},
 			setup: func() {},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, 1, len(command.conf.Instances))
-				assert(t, true, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, 1, len(c.conf.Instances))
+				assert(t, true, c.conf.Debug)
+				assert(t, 5555, c.conf.Port)
+				assert(t, true, c.conf.DebugLogs)
+				assert(t, true, c.conf.IAMAuthN)
 			},
 		},
 		{
 			desc:  "yaml config file",
-			args:  []string{"--config-file", "testdata/config.yaml"},
+			args:  []string{"--config-file", "testdata/config-yaml.yaml"},
 			setup: func() {},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, 1, len(command.conf.Instances))
-				assert(t, true, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, 1, len(c.conf.Instances))
+				assert(t, true, c.conf.Debug)
 			},
 		},
 		{
 			desc:  "json config file",
-			args:  []string{"--config-file", "testdata/config.json"},
+			args:  []string{"--config-file", "testdata/config-json.json"},
 			setup: func() {},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, 1, len(command.conf.Instances))
-				assert(t, true, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, 1, len(c.conf.Instances))
+				assert(t, true, c.conf.Debug)
 			},
 		},
 		{
 			desc:  "config file with two instances",
 			args:  []string{"--config-file", "testdata/two-instances.toml"},
 			setup: func() {},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, 2, len(command.conf.Instances))
+			assert: func(t *testing.T, c *Command) {
+				assert(t, 2, len(c.conf.Instances))
 			},
 		},
 		{
@@ -73,8 +76,8 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			setup: func() {
 				t.Setenv("CSQL_PROXY_INSTANCE_CONNECTION_NAME", "p:r:i")
 			},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, "proj:region:inst", command.conf.Instances[0].Name)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, "proj:region:inst", c.conf.Instances[0].Name)
 			},
 		},
 		{
@@ -83,8 +86,8 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			setup: func() {
 				t.Setenv("CSQL_PROXY_INSTANCE_CONNECTION_NAME", "p:r:i")
 			},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, "p:r:i", command.conf.Instances[0].Name)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, "p:r:i", c.conf.Instances[0].Name)
 			},
 		},
 		{
@@ -93,8 +96,8 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			setup: func() {
 				t.Setenv("CSQL_PROXY_DEBUG", "false")
 			},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, true, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, true, c.conf.Debug)
 			},
 		},
 		{
@@ -105,8 +108,8 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 				"--debug",
 			},
 			setup: func() {},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, true, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, true, c.conf.Debug)
 			},
 		},
 		{
@@ -118,8 +121,8 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			setup: func() {
 				t.Setenv("CSQL_PROXY_DEBUG", "false")
 			},
-			assert: func(t *testing.T, command *Command) {
-				assert(t, false, command.conf.Debug)
+			assert: func(t *testing.T, c *Command) {
+				assert(t, false, c.conf.Debug)
 			},
 		},
 	}
diff --git a/cmd/root.go b/cmd/root.go
index d95b63402..28a48213a 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -258,20 +258,21 @@ Configuration using a configuration file
 
   The configuration file may look like the following:
 
-      instance_connection_name = "my-project:us-central1:my-server-instance"
+      instance-connection-name = "my-project:us-central1:my-server-instance"
+      auto-iam-authn = true
 
   If multiple instance connection names are used, add the index of the
   instance connection name as a suffix. For example:
 
-      instance_connection_name_0 = "my-project:us-central1:my-db-server"
-      instance_connection_name_1 = "my-other-project:us-central1:my-other-server"
+      instance-connection-name-0 = "my-project:us-central1:my-db-server"
+      instance-connection-name-1 = "my-other-project:us-central1:my-other-server"
 
   The configuration file may also contain the same keys as the environment
   variables and flags. For example:
 
-      auto_iam_authn = true
+      auto-iam-authn = true
       debug = true
-      max_connections = 5
+      max-connections = 5
 
 Localhost Admin Server
 
@@ -532,8 +533,6 @@ func loadConfig(c *Command, args []string, opts []Option) error {
 		return err
 	}
 
-	_ = v.BindPFlags(c.Flags())
-
 	c.Flags().VisitAll(func(f *pflag.Flag) {
 		// Override any unset flags with Viper values to use the pflags
 		// object as a single source of truth.
@@ -661,10 +660,10 @@ func instanceFromEnv(args []string) []string {
 
 func instanceFromConfigFile(v *viper.Viper) []string {
 	var args []string
-	inst := v.GetString("instance_connection_name")
+	inst := v.GetString("instance-connection-name")
 
 	if inst == "" {
-		inst = v.GetString("instance_connection_name_0")
+		inst = v.GetString("instance-connection-name-0")
 		if inst == "" {
 			return nil
 		}
@@ -673,7 +672,7 @@ func instanceFromConfigFile(v *viper.Viper) []string {
 
 	i := 1
 	for {
-		instN := v.GetString(fmt.Sprintf("instance_connection_name_%d", i))
+		instN := v.GetString(fmt.Sprintf("instance-connection-name-%d", i))
 		// if the next instance connection name is not defined, stop checking
 		// environment variables.
 		if instN == "" {
diff --git a/cmd/testdata/config-json.json b/cmd/testdata/config-json.json
new file mode 100644
index 000000000..6a8ea08dc
--- /dev/null
+++ b/cmd/testdata/config-json.json
@@ -0,0 +1,4 @@
+{
+  "instance-connection-name": "proj:region:inst",
+  "debug": true
+}
diff --git a/cmd/testdata/config-toml.toml b/cmd/testdata/config-toml.toml
new file mode 100644
index 000000000..2cad8bc6b
--- /dev/null
+++ b/cmd/testdata/config-toml.toml
@@ -0,0 +1,5 @@
+instance-connection-name = "proj:region:inst"
+debug = true
+port = "5555"
+debug-logs = true
+auto-iam-authn = true
diff --git a/cmd/testdata/config.yaml b/cmd/testdata/config-yaml.yaml
similarity index 92%
rename from cmd/testdata/config.yaml
rename to cmd/testdata/config-yaml.yaml
index 45410ba6d..4ab85f439 100644
--- a/cmd/testdata/config.yaml
+++ b/cmd/testdata/config-yaml.yaml
@@ -12,5 +12,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-instance_connection_name: "proj:region:inst"
+instance-connection-name: "proj:region:inst"
 debug: true
diff --git a/cmd/testdata/config.json b/cmd/testdata/config.json
deleted file mode 100644
index 5eeaa3e1a..000000000
--- a/cmd/testdata/config.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "instance_connection_name": "proj:region:inst",
-  "debug": true
-}
diff --git a/cmd/testdata/config.toml b/cmd/testdata/config.toml
deleted file mode 100644
index 0fae09451..000000000
--- a/cmd/testdata/config.toml
+++ /dev/null
@@ -1,2 +0,0 @@
-instance_connection_name = "proj:region:inst"
-debug = true
diff --git a/cmd/testdata/two-instances.toml b/cmd/testdata/two-instances.toml
index fa46556c8..ddd670f5e 100644
--- a/cmd/testdata/two-instances.toml
+++ b/cmd/testdata/two-instances.toml
@@ -1,2 +1,2 @@
-instance_connection_name_0 = "x:y:z"
-instance_connection_name_1 = "a:b:c"
+instance-connection-name-0 = "x:y:z"
+instance-connection-name-1 = "a:b:c"