diff --git a/api/filters/nameref/nameref.go b/api/filters/nameref/nameref.go
index 4815f10a29..ff83420cb1 100644
--- a/api/filters/nameref/nameref.go
+++ b/api/filters/nameref/nameref.go
@@ -284,9 +284,9 @@ func (f Filter) roleRefFilter() sieveFunc {
 	return previousIdSelectedByGvk(roleRefGvk)
 }
 
-func prefixSuffixEquals(other resource.ResCtx) sieveFunc {
+func prefixSuffixEquals(other resource.ResCtx, allowEmpty bool) sieveFunc {
 	return func(r *resource.Resource) bool {
-		return r.PrefixesSuffixesEquals(other)
+		return r.PrefixesSuffixesEquals(other, allowEmpty)
 	}
 }
 
@@ -325,7 +325,10 @@ func (f Filter) selectReferral(
 	if len(candidates) == 1 {
 		return candidates[0], nil
 	}
-	candidates = doSieve(candidates, prefixSuffixEquals(f.Referrer))
+	candidates = doSieve(candidates, prefixSuffixEquals(f.Referrer, true))
+	if len(candidates) > 1 {
+		candidates = doSieve(candidates, prefixSuffixEquals(f.Referrer, false))
+	}
 	if len(candidates) == 1 {
 		return candidates[0], nil
 	}
diff --git a/api/krusty/configmaps_test.go b/api/krusty/configmaps_test.go
index b161d88b35..e36767fa74 100644
--- a/api/krusty/configmaps_test.go
+++ b/api/krusty/configmaps_test.go
@@ -591,3 +591,184 @@ metadata:
   name: test-m8t7bmb6g2
 `)
 }
+
+// Regression test for https://github.com/kubernetes-sigs/kustomize/issues/5047
+func TestPrefixSuffix(t *testing.T) {
+	th := kusttest_test.MakeHarness(t)
+	th.WriteF("kustomization.yaml", `
+resources:
+- a
+- b
+`)
+
+	th.WriteF("a/kustomization.yaml", `
+resources:
+- ../common
+
+namePrefix: a
+`)
+
+	th.WriteF("b/kustomization.yaml", `
+resources:
+- ../common
+
+namePrefix: b
+`)
+
+	th.WriteF("common/kustomization.yaml", `
+resources:
+- service
+
+configMapGenerator:
+- name: "-example-configmap"
+`)
+
+	th.WriteF("common/service/deployment.yaml", `
+kind: Deployment
+apiVersion: apps/v1
+
+metadata:
+  name: "-"
+
+spec:
+  template:
+    spec:
+      containers:
+      - name: app
+        envFrom:
+        - configMapRef:
+            name: "-example-configmap"
+`)
+
+	th.WriteF("common/service/kustomization.yaml", `
+resources:
+- deployment.yaml
+
+nameSuffix: api
+`)
+
+	m := th.Run(".", th.MakeDefaultOptions())
+	th.AssertActualEqualsExpected(m, `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: a-api
+spec:
+  template:
+    spec:
+      containers:
+      - envFrom:
+        - configMapRef:
+            name: a-example-configmap-6ct58987ht
+        name: app
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: a-example-configmap-6ct58987ht
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: b-api
+spec:
+  template:
+    spec:
+      containers:
+      - envFrom:
+        - configMapRef:
+            name: b-example-configmap-6ct58987ht
+        name: app
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: b-example-configmap-6ct58987ht
+`)
+}
+
+// Regression test for https://github.com/kubernetes-sigs/kustomize/issues/5047
+func TestPrefixSuffix2(t *testing.T) {
+	th := kusttest_test.MakeHarness(t)
+	th.WriteF("kustomization.yaml", `
+resources:
+- a
+- b
+`)
+
+	th.WriteF("a/kustomization.yaml", `
+resources:
+- ../common
+
+namePrefix: a
+`)
+
+	th.WriteF("b/kustomization.yaml", `
+resources:
+- ../common
+
+namePrefix: b
+`)
+
+	th.WriteF("common/deployment.yaml", `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: "-example"
+spec:
+  template:
+    spec:
+      containers:
+      - name: app
+        envFrom:
+        - configMapRef:
+            name: "-example-configmap"
+`)
+
+	th.WriteF("common/kustomization.yaml", `
+resources:
+- deployment.yaml
+
+configMapGenerator:
+- name: "-example-configmap"
+`)
+
+	m := th.Run(".", th.MakeDefaultOptions())
+	th.AssertActualEqualsExpected(m, `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: a-example
+spec:
+  template:
+    spec:
+      containers:
+      - envFrom:
+        - configMapRef:
+            name: a-example-configmap-6ct58987ht
+        name: app
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: a-example-configmap-6ct58987ht
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: b-example
+spec:
+  template:
+    spec:
+      containers:
+      - envFrom:
+        - configMapRef:
+            name: b-example-configmap-6ct58987ht
+        name: app
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: b-example-configmap-6ct58987ht
+`)
+}
diff --git a/api/resource/resource.go b/api/resource/resource.go
index ae1a98be0e..9884a672c5 100644
--- a/api/resource/resource.go
+++ b/api/resource/resource.go
@@ -287,12 +287,25 @@ func (r *Resource) getCsvAnnotation(name string) []string {
 	return strings.Split(annotations[name], ",")
 }
 
-// PrefixesSuffixesEquals is conceptually doing the same task
-// as OutermostPrefixSuffix but performs a deeper comparison
-// of the suffix and prefix slices.
-func (r *Resource) PrefixesSuffixesEquals(o ResCtx) bool {
-	return utils.SameEndingSubSlice(r.GetNamePrefixes(), o.GetNamePrefixes()) &&
-		utils.SameEndingSubSlice(r.GetNameSuffixes(), o.GetNameSuffixes())
+// PrefixesSuffixesEquals is conceptually doing the same task as
+// OutermostPrefixSuffix but performs a deeper comparison of the suffix and
+// prefix slices.
+// The allowEmpty flag determines whether an empty prefix/suffix
+// should be considered a match on anything.
+// This is used when filtering, starting with a coarser pass allowing empty
+// matches, before requiring exact matches if there are multiple
+// remaining candidates.
+func (r *Resource) PrefixesSuffixesEquals(o ResCtx, allowEmpty bool) bool {
+	if allowEmpty {
+		eitherPrefixEmpty := len(r.GetNamePrefixes()) == 0 || len(o.GetNamePrefixes()) == 0
+		eitherSuffixEmpty := len(r.GetNameSuffixes()) == 0 || len(o.GetNameSuffixes()) == 0
+
+		return (eitherPrefixEmpty || utils.SameEndingSubSlice(r.GetNamePrefixes(), o.GetNamePrefixes())) &&
+			(eitherSuffixEmpty || utils.SameEndingSubSlice(r.GetNameSuffixes(), o.GetNameSuffixes()))
+	} else {
+		return utils.SameEndingSubSlice(r.GetNamePrefixes(), o.GetNamePrefixes()) &&
+			utils.SameEndingSubSlice(r.GetNameSuffixes(), o.GetNameSuffixes())
+	}
 }
 
 // RemoveBuildAnnotations removes annotations created by the build process.