diff --git a/api/config.go b/api/config.go
index d0e15604..b10438ea 100644
--- a/api/config.go
+++ b/api/config.go
@@ -27,7 +27,7 @@ func NewConfig(connection string) Config {
 type Config struct {
 	Metrics                  bool
 	ConnectionString, Schema string
-	RunMigrations            bool // Deprecated
+	RunMigrations            bool
 	SkipMigrations           bool
 	SkipMigrationFiles       []string
 	DisableKubernetes        bool
@@ -37,6 +37,18 @@ type Config struct {
 	LogName                  string
 }
 
+func (t *Config) Migrate() bool {
+	// We have two flags dictating whether to run migration or not
+	// depending on whether it's being used on mission-control or (config-db/canary-checker).
+	// Prioritize SkipMigrations over RunMigrations.
+
+	if t.SkipMigrations {
+		return false
+	}
+
+	return t.RunMigrations
+}
+
 func PrintableSecret(secret string) string {
 	if len(secret) == 0 {
 		return "<nil>"
@@ -72,7 +84,7 @@ func (c Config) ReadEnv() Config {
 }
 
 func (c Config) String() string {
-	s := fmt.Sprintf("migrate=%v log=%v postgrest=(%s)", !c.SkipMigrations, c.LogLevel, c.Postgrest.String())
+	s := fmt.Sprintf("migrate=%v log=%v postgrest=(%s)", c.Migrate(), c.LogLevel, c.Postgrest.String())
 	if pgUrl, err := url.Parse(c.ConnectionString); err == nil {
 		s = fmt.Sprintf("url=%s ", pgUrl.Redacted()) + s
 	}
diff --git a/db.go b/db.go
index 83d7b441..43eb7cc4 100644
--- a/db.go
+++ b/db.go
@@ -213,7 +213,7 @@ func SetupDB(config api.Config) (gormDB *gorm.DB, pgxpool *pgxpool.Pool, err err
 		return
 	}
 
-	if !config.SkipMigrations {
+	if config.Migrate() {
 		if err = Migrate(config); err != nil {
 			return
 		}
diff --git a/start.go b/start.go
index f58dabd9..e2b88667 100644
--- a/start.go
+++ b/start.go
@@ -20,15 +20,17 @@ import (
 	"gorm.io/plugin/prometheus"
 )
 
-func BindPFlags(flags *pflag.FlagSet) {
+type BindFlagOption struct {
+	SkipMigrationByDefault bool
+}
+
+func BindPFlags(flags *pflag.FlagSet, opt BindFlagOption) {
 	_ = flags.MarkDeprecated("postgrest-anon-role", "Use postgrest-role instead")
 	flags.StringVar(&DefaultConfig.ConnectionString, "db", "DB_URL", "Connection string for the postgres database")
 	flags.StringVar(&DefaultConfig.Schema, "db-schema", "public", "Postgres schema")
 	flags.StringVar(&DefaultConfig.Postgrest.URL, "postgrest-uri", "http://localhost:3000", "URL for the PostgREST instance to use. If localhost is supplied, a PostgREST instance will be started")
 	flags.StringVar(&DefaultConfig.Postgrest.LogLevel, "postgrest-log-level", "info", "PostgREST log level")
 	flags.StringVar(&DefaultConfig.Postgrest.JWTSecret, "postgrest-jwt-secret", "PGRST_JWT_SECRET", "JWT Secret Token for PostgREST")
-	flags.BoolVar(&DefaultConfig.RunMigrations, "db-migrations", true, "Run database migrations")
-	flags.BoolVar(&DefaultConfig.SkipMigrations, "skip-migrations", false, "Skip database migrations")
 	flags.BoolVar(&DefaultConfig.Postgrest.Disable, "disable-postgrest", false, "Disable PostgREST. Deprecated (Use --postgrest-uri '' to disable PostgREST)")
 	flags.StringVar(&DefaultConfig.Postgrest.DBRole, "postgrest-role", "postgrest_api", "PostgREST role for authentication connections")
 	flags.IntVar(&DefaultConfig.Postgrest.MaxRows, "postgrest-max-rows", 2000, "A hard limit to the number of rows PostgREST will fetch")
@@ -36,7 +38,14 @@ func BindPFlags(flags *pflag.FlagSet) {
 	flags.BoolVar(&DefaultConfig.DisableKubernetes, "disable-kubernetes", false, "Disable Kubernetes integration")
 	flags.BoolVar(&DefaultConfig.Metrics, "db-metrics", false, "Expose db metrics")
 
-	_ = flags.MarkDeprecated("db-migrations", "migrations are run by default. Use --skip-migrations to skip migrations.")
+	if opt.SkipMigrationByDefault {
+		flags.BoolVar(&DefaultConfig.RunMigrations, "db-migrations", false, "Run database migrations")
+		DefaultConfig.SkipMigrations = false // pratically disable this flag so RunMigrations dictates migration
+	} else {
+		flags.BoolVar(&DefaultConfig.SkipMigrations, "skip-migrations", false, "Skip database migrations")
+		flags.BoolVar(&DefaultConfig.RunMigrations, "db-migrations", true, "Run database migrations")
+		_ = flags.MarkDeprecated("db-migrations", "migrations are run by default. Use --skip-migrations to skip migrations.")
+	}
 }
 
 type StartOption func(config Config) Config
@@ -65,12 +74,14 @@ var EnableMetrics = func(config Config) Config {
 
 var SkipMigrations = func(config Config) Config {
 	config.SkipMigrations = true
+	config.RunMigrations = false
 	return config
 }
 
 var ClientOnly = func(config Config) Config {
 	config.Postgrest.Disable = true
 	config.SkipMigrations = true
+	config.RunMigrations = false
 	return config
 }