diff --git a/cmd/ci-operator-prowgen/main.go b/cmd/ci-operator-prowgen/main.go
index 10916206e5c..b05bf155607 100644
--- a/cmd/ci-operator-prowgen/main.go
+++ b/cmd/ci-operator-prowgen/main.go
@@ -8,16 +8,16 @@ import (
 	"regexp"
 	"strings"
 
-	"github.com/openshift/ci-tools/pkg/promotion"
 	"github.com/sirupsen/logrus"
+	kubeapi "k8s.io/api/core/v1"
+	"k8s.io/apimachinery/pkg/api/resource"
 	"k8s.io/test-infra/prow/apis/prowjobs/v1"
+	prowconfig "k8s.io/test-infra/prow/config"
 
 	cioperatorapi "github.com/openshift/ci-tools/pkg/api"
 	"github.com/openshift/ci-tools/pkg/config"
 	jc "github.com/openshift/ci-tools/pkg/jobconfig"
-	kubeapi "k8s.io/api/core/v1"
-	"k8s.io/apimachinery/pkg/api/resource"
-	prowconfig "k8s.io/test-infra/prow/config"
+	"github.com/openshift/ci-tools/pkg/promotion"
 )
 
 const (
@@ -112,6 +112,11 @@ func (o *options) process() error {
 		return fmt.Errorf("ci-operator-prowgen needs exactly one of `--from-{file,dir,release-repo}` options")
 	}
 
+	if o.fromFile != "" {
+		logrus.Info("--from-file implies --prune=false to avoid clobbering jobs")
+		o.prune = false
+	}
+
 	if o.toDir == "" {
 		return fmt.Errorf("ci-operator-prowgen needs exactly one of `--to-{dir,release-repo}` options")
 	}