diff --git a/cmd/cert-checker/main.go b/cmd/cert-checker/main.go
index 1164aebce..182b17f79 100644
--- a/cmd/cert-checker/main.go
+++ b/cmd/cert-checker/main.go
@@ -332,11 +332,13 @@ type config struct {
 
 func main() {
 	configFile := flag.String("config", "", "File path to the configuration file for this service")
-	workers := flag.Int("workers", runtime.NumCPU(), "The number of concurrent workers used to process certificates")
-	badResultsOnly := flag.Bool("bad-results-only", false, "Only collect and display bad results")
-	connect := flag.String("db-connect", "", "SQL URI if not provided in the configuration file")
-	cp := flag.Duration("check-period", time.Hour*2160, "How far back to check")
-	unexpiredOnly := flag.Bool("unexpired-only", false, "Only check currently unexpired certificates")
+
+	// TODO(#5489): Remove these deprecated flags.
+	_ = flag.Int("workers", runtime.NumCPU(), "The number of concurrent workers used to process certificates")
+	_ = flag.Bool("bad-results-only", false, "Only collect and display bad results")
+	_ = flag.String("db-connect", "", "SQL URI if not provided in the configuration file")
+	_ = flag.Duration("check-period", time.Hour*2160, "How far back to check")
+	_ = flag.Bool("unexpired-only", false, "Only check currently unexpired certificates")
 
 	flag.Parse()
 	if *configFile == "" {
@@ -358,16 +360,6 @@ func main() {
 	err = blog.Set(logger)
 	cmd.FailOnError(err, "Failed to set audit logger")
 
-	if *connect != "" {
-		config.CertChecker.DB.DBConnect = *connect
-	}
-	if *workers != 0 {
-		config.CertChecker.Workers = *workers
-	}
-	config.CertChecker.UnexpiredOnly = *unexpiredOnly
-	config.CertChecker.BadResultsOnly = *badResultsOnly
-	config.CertChecker.CheckPeriod.Duration = *cp
-
 	avps := make(map[uint]bool)
 	if len(config.CertChecker.AcceptableValidityPeriods) == 0 {
 		// For backwards compatibility, assume only a single valid validity period
diff --git a/test/config/cert-checker.json b/test/config/cert-checker.json
index 338cad328..03b66070e 100644
--- a/test/config/cert-checker.json
+++ b/test/config/cert-checker.json
@@ -5,6 +5,10 @@
       "maxOpenConns": 10
     },
     "hostnamePolicyFile": "test/hostname-policy.yaml",
+    "workers": 16,
+    "unexpiredOnly": true,
+    "badResultsOnly": true,
+    "checkPeriod": "72h",
     "acceptableValidityPeriods": [7775999, 7776000],
     "ignoredLints": [
       "n_subject_common_name_included"