diff --git a/config.go b/config.go
index e2178b7d..add43823 100644
--- a/config.go
+++ b/config.go
@@ -116,6 +116,9 @@ func (c *Config) OverrideByOption(opt *Option) {
 	if opt.Timeout != nil {
 		c.Timeout = &Duration{*opt.Timeout}
 	}
+	if opt.FilterCommand != "" {
+		c.FilterCommand = opt.FilterCommand
+	}
 }
 
 // Restrict restricts a configuration.
@@ -164,9 +167,8 @@ func (c *Config) Restrict(ctx context.Context) error {
 	if err := c.setupPlugins(ctx); err != nil {
 		return fmt.Errorf("failed to setup plugins: %w", err)
 	}
-
 	if c.FilterCommand != "" {
-		Log("[WARNING] filter_command is deprecated. Use %s environment variable instead.", FilterCommandEnv)
+		Log("[WARNING] filter_command is deprecated. Use environment variable or CLI flag instead.")
 	}
 	return nil
 }
diff --git a/config_test.go b/config_test.go
index 39b69609..51d17c75 100644
--- a/config_test.go
+++ b/config_test.go
@@ -311,9 +311,9 @@ var FilterCommandTests = []struct {
 func TestFilterCommandDeprecated(t *testing.T) {
 	ctx := context.Background()
 	for _, ts := range FilterCommandTests {
-		t.Setenv("ECSPRESSO_FILTER_COMMAND", ts.Env)
 		app, err := ecspresso.New(ctx, &ecspresso.Option{
 			ConfigFilePath: "tests/filter_command.yml",
+			FilterCommand:  ts.Env,
 		})
 		if err != nil {
 			t.Error(err)
diff --git a/ecspresso.go b/ecspresso.go
index 23b6668d..3c2a9abb 100644
--- a/ecspresso.go
+++ b/ecspresso.go
@@ -31,7 +31,6 @@ import (
 const DefaultDesiredCount = -1
 const DefaultConfigFilePath = "ecspresso.yml"
 const dryRunStr = "DRY RUN"
-const FilterCommandEnv = "ECSPRESSO_FILTER_COMMAND"
 
 var Version string
 var delayForServiceChanged = 3 * time.Second
@@ -184,6 +183,7 @@ type Option struct {
 	ConfigFilePath string            `name:"config" help:"config file" default:"ecspresso.yml" env:"ECSPRESSO_CONFIG"`
 	AssumeRoleARN  string            `help:"the ARN of the role to assume" default:"" env:"ECSPRESSO_ASSUME_ROLE_ARN"`
 	Timeout        *time.Duration    `help:"timeout. Override in a configuration file." env:"ECSPRESSO_TIMEOUT"`
+	FilterCommand  string            `help:"filter command" env:"ECSPRESSO_FILTER_COMMAND"`
 }
 
 func (opt *Option) resolveConfigFilePath() (path string) {
@@ -538,8 +538,5 @@ func (d *App) GetLogInfo(task *types.Task, c *types.ContainerDefinition) (string
 }
 
 func (d *App) FilterCommand() string {
-	if fc := os.Getenv(FilterCommandEnv); fc != "" {
-		return fc
-	}
 	return d.config.FilterCommand
 }