diff --git a/cmd/config_test.go b/cmd/config_test.go
index 8b252dff5..f5e029c40 100644
--- a/cmd/config_test.go
+++ b/cmd/config_test.go
@@ -82,7 +82,7 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 		},
 		{
 			desc: "instance env overrides config file precedence",
-			args: []string{"--config-file", "testdata/config.json"},
+			args: []string{"--config-file", "testdata/config-json.json"},
 			setup: func() {
 				t.Setenv("CSQL_PROXY_INSTANCE_CONNECTION_NAME", "p:r:i")
 			},
@@ -104,7 +104,7 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			desc: "flag overrides config file precedence",
 			args: []string{
 				"proj:region:inst",
-				"--config-file", "testdata/config.toml",
+				"--config-file", "testdata/config-toml.toml",
 				"--debug",
 			},
 			setup: func() {},
@@ -116,7 +116,7 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 			desc: "env overrides config file precedence",
 			args: []string{
 				"proj:region:inst",
-				"--config-file", "testdata/config.toml",
+				"--config-file", "testdata/config-toml.toml",
 			},
 			setup: func() {
 				t.Setenv("CSQL_PROXY_DEBUG", "false")
@@ -125,6 +125,20 @@ func TestNewCommandWithConfigFile(t *testing.T) {
 				assert(t, false, c.conf.Debug)
 			},
 		},
+		{
+			desc: "specific config file extension prioritization",
+			args: []string{
+				"proj:region:inst",
+				"--config-file", "testdata/priority.toml",
+			},
+			setup: func() {},
+			assert: func(t *testing.T, c *Command) {
+				// priority.toml has max-connections = 5555 and port = 5555
+				// priority.json has max-connections = 6666 and port = 6666
+				assert(t, uint64(5555), c.conf.MaxConnections)
+				assert(t, 5555, c.conf.Port)
+			},
+		},
 	}
 
 	for _, tc := range tcs {
diff --git a/cmd/root.go b/cmd/root.go
index 4b0ab1a56..319ab675a 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -666,10 +666,6 @@ func initViper(c *Command) (*viper.Viper, error) {
 	v := viper.New()
 
 	if c.conf.Filepath != "" {
-		// Setup Viper configuration file. Viper will attempt to load
-		// configuration from the specified file if it exists. Otherwise, Viper
-		// will source all configuration from flags and then environment
-		// variables.
 		ext := filepath.Ext(c.conf.Filepath)
 
 		badExtErr := newBadCommandError(
@@ -685,11 +681,7 @@ func initViper(c *Command) (*viper.Viper, error) {
 			return nil, badExtErr
 		}
 
-		conf := filepath.Base(c.conf.Filepath)
-		noExt := strings.ReplaceAll(conf, ext, "")
-		// argument must be the name of config file without extension
-		v.SetConfigName(noExt)
-		v.AddConfigPath(filepath.Dir(c.conf.Filepath))
+		v.SetConfigFile(c.conf.Filepath)
 
 		// Attempt to load configuration from a file. If no file is found,
 		// assume configuration is provided by flags or environment variables.
diff --git a/cmd/testdata/priority.json b/cmd/testdata/priority.json
new file mode 100644
index 000000000..705f52c65
--- /dev/null
+++ b/cmd/testdata/priority.json
@@ -0,0 +1,4 @@
+{
+  "max-connections": 6666,
+  "port": 6666
+}
diff --git a/cmd/testdata/priority.toml b/cmd/testdata/priority.toml
new file mode 100644
index 000000000..7420ab7b0
--- /dev/null
+++ b/cmd/testdata/priority.toml
@@ -0,0 +1,2 @@
+max-connections = 5555
+port = 5555