diff --git a/pkg/controller/jaeger/jaeger_controller.go b/pkg/controller/jaeger/jaeger_controller.go
index 5c31bac87d..3ea26be544 100644
--- a/pkg/controller/jaeger/jaeger_controller.go
+++ b/pkg/controller/jaeger/jaeger_controller.go
@@ -10,6 +10,7 @@ import (
 	"github.com/pkg/errors"
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/viper"
+	appsv1 "k8s.io/api/apps/v1"
 	corev1 "k8s.io/api/core/v1"
 	k8serrors "k8s.io/apimachinery/pkg/api/errors"
 	"k8s.io/apimachinery/pkg/runtime"
@@ -21,6 +22,7 @@ import (
 	"sigs.k8s.io/controller-runtime/pkg/source"
 
 	"github.com/jaegertracing/jaeger-operator/pkg/apis/jaegertracing/v1"
+	"github.com/jaegertracing/jaeger-operator/pkg/inject"
 	"github.com/jaegertracing/jaeger-operator/pkg/strategy"
 )
 
@@ -220,5 +222,29 @@ func (r *ReconcileJaeger) apply(jaeger v1.Jaeger, str strategy.S) error {
 		}
 	}
 
+	if err := r.scanDeployments(jaeger); err != nil {
+		return err
+	}
+
+	return nil
+}
+
+func (r *ReconcileJaeger) scanDeployments(jaeger v1.Jaeger) error {
+	pods := &v1.JaegerList{}
+	deps := &appsv1.DeploymentList{}
+
+	opts := &client.ListOptions{}
+	if err := r.client.List(context.Background(), opts, pods); err != nil {
+		return err
+	}
+	if err := r.client.List(context.Background(), opts, deps); err != nil {
+		return err
+	}
+	injectedDeps := inject.RequireInjections(&jaeger, pods, deps)
+	for _, d := range injectedDeps {
+		if err := r.client.Update(context.Background(), d); err != nil {
+			return err
+		}
+	}
 	return nil
 }
diff --git a/pkg/inject/sidecar.go b/pkg/inject/sidecar.go
index c6ff52fef0..92dd83a4ea 100644
--- a/pkg/inject/sidecar.go
+++ b/pkg/inject/sidecar.go
@@ -177,3 +177,34 @@ func hasEnv(name string, vars []corev1.EnvVar) bool {
 	}
 	return false
 }
+
+// RequireInjections deployments
+func RequireInjections(jaeger *v1.Jaeger, pods *v1.JaegerList, deps *appsv1.DeploymentList) []*appsv1.Deployment {
+	requireUpdates := make([]*appsv1.Deployment, 0)
+	for i := 0; i < len(deps.Items); i++ {
+		dep := &deps.Items[i]
+		if Needed(dep) {
+			if belongsToJaegerInstance(dep, jaeger, len(pods.Items) == 1) {
+				// a suitable jaeger instance was found! let's inject a sidecar pointing to it then
+				log.WithFields(log.Fields{
+					"deployment":       dep.Name,
+					"namespace":        dep.Namespace,
+					"jaeger":           jaeger.Name,
+					"jaeger-namespace": jaeger.Namespace,
+				}).Info("Injecting Jaeger Agent sidecar")
+				dep.Annotations[Annotation] = jaeger.Name
+				newDep := Sidecar(jaeger, dep)
+				requireUpdates = append(requireUpdates, newDep)
+			} else {
+				log.WithField("deployment", dep.Name).Info("No suitable Jaeger instances found to inject a sidecar")
+			}
+		}
+	}
+	return requireUpdates
+}
+
+func belongsToJaegerInstance(dep *appsv1.Deployment, instance *v1.Jaeger, uniqueInstance bool) bool {
+	annotation := dep.Annotations[Annotation]
+	return strings.EqualFold(annotation, "true") &&
+		uniqueInstance || annotation == instance.Name
+}