diff --git a/typed/remove.go b/typed/remove.go
index 86de5105..253f3ba9 100644
--- a/typed/remove.go
+++ b/typed/remove.go
@@ -80,22 +80,23 @@ func (w *removingWalker) doList(t *schema.List) (errs ValidationErrors) {
 		path, _ := fieldpath.MakePath(pe)
 		// save items on the path when we shouldExtract
 		// but ignore them when we are removing (i.e. !w.shouldExtract)
-		if w.toRemove.Has(path) {
-			if w.shouldExtract {
-				newItems = append(newItems, removeItemsWithSchema(item, w.toRemove, w.schema, t.ElementType, w.shouldExtract).Unstructured())
-			} else {
-				continue
+		if w.shouldExtract {
+			if w.toRemove.Has(path) || !w.toRemove.WithPrefix(pe).Empty() {
+				if !w.toRemove.WithPrefix(pe).Empty() {
+					// Continue if there are subset paths
+					item = removeItemsWithSchema(item, w.toRemove.WithPrefix(pe), w.schema, t.ElementType, w.shouldExtract)
+				}
+				newItems = append(newItems, item.Unstructured())
 			}
-		}
-		if subset := w.toRemove.WithPrefix(pe); !subset.Empty() {
-			item = removeItemsWithSchema(item, subset, w.schema, t.ElementType, w.shouldExtract)
 		} else {
-			// don't save items not on the path when we shouldExtract.
-			if w.shouldExtract {
+			if w.toRemove.Has(path) {
 				continue
 			}
+			if !w.toRemove.WithPrefix(pe).Empty() {
+				item = removeItemsWithSchema(item, w.toRemove.WithPrefix(pe), w.schema, t.ElementType, w.shouldExtract)
+			}
+			newItems = append(newItems, item.Unstructured())
 		}
-		newItems = append(newItems, item.Unstructured())
 	}
 	if len(newItems) > 0 {
 		w.out = newItems
diff --git a/typed/remove_test.go b/typed/remove_test.go
index 2cb469dc..0109aff4 100644
--- a/typed/remove_test.go
+++ b/typed/remove_test.go
@@ -941,6 +941,92 @@ var extractWithKeysCases = []extractWithKeysTestCase{{
 			},
 		},
 	},
+}, {
+	name:         "atomicStructures",
+	rootTypeName: "myRoot",
+	schema:       typed.YAMLObject(associativeAndAtomicSchema),
+	triplets: []extractTriplet{
+		{
+			// extract from atomic list should return entire list
+			object: `{"atomicList":["a", "b", "c"]}`,
+			set: _NS(
+				_P("atomicList", _V("b")),
+			),
+			wantOutput: typed.YAMLObject(`{"atomicList":["a", "b", "c"]}`),
+		},
+		{
+			// extract from atomic map should return entire map
+			object: `{"atomicMap":{"key1": "value1", "key2": "value2"}}`,
+			set: _NS(
+				_P("atomicMap", "key1"),
+			),
+			wantOutput: typed.YAMLObject(`{"atomicMap":{"key1": "value1", "key2": "value2"}}`),
+		},
+		{
+			// extract with both atomic and associative structures
+			object: `{"list":[{"key":"nginx","id":1,"nv":2}], "atomicList":["x", "y"]}`,
+			set: _NS(
+				_P("list", _KBF("key", "nginx", "id", 1), "nv"),
+				_P("atomicList", _V("x")),
+			),
+			wantOutput: typed.YAMLObject(`{"list":[{"key":"nginx","id":1, "nv":2}], "atomicList":["x", "y"]}`),
+		},
+	},
+}, {
+	name:         "compositeKeysExtraction",
+	rootTypeName: "myRoot",
+	schema:       typed.YAMLObject(associativeAndAtomicSchema),
+	triplets: []extractTriplet{
+		{
+			// extract with composite keys - partial field extraction
+			object: `{"list":[{"key":"a","id":1,"nv":2,"bv":true},{"key":"a","id":2,"nv":3}]}`,
+			set: _NS(
+				_P("list", _KBF("key", "a", "id", 1), "nv"),
+			),
+			wantOutput: typed.YAMLObject(`{"list":[{"key":"a","id":1,"nv":2}]}`),
+		},
+		{
+			// This test case specifically catches the bug where WithAppendKeyFields
+			// would duplicate items when extracting with both item key and field paths
+			object: `{"list":[{"key":"nginx","id":1,"nv":2,"bv":true},{"key":"apache","id":2,"nv":3}]}`,
+			set: _NS(
+				_P("list", _KBF("key", "nginx", "id", 1)),
+				_P("list", _KBF("key", "nginx", "id", 1), "nv"),
+			),
+			wantOutput: typed.YAMLObject(`{"list":[{"key":"nginx","id":1,"nv":2}]}`),
+		},
+		{
+			// extract multiple items with composite keys
+			object: `{"list":[{"key":"a","id":1,"nv":2},{"key":"a","id":2,"nv":3},{"key":"b","id":1,"nv":4}]}`,
+			set: _NS(
+				_P("list", _KBF("key", "a", "id", 1)),
+				_P("list", _KBF("key", "b", "id", 1)),
+			),
+			wantOutput: typed.YAMLObject(`{"list":[{"key":"a","id":1},{"key":"b","id":1}]}`),
+		},
+	},
+}, {
+	name:         "nestedListsPartialExtraction",
+	rootTypeName: "type",
+	schema:       typed.YAMLObject(nestedTypesSchema),
+	triplets: []extractTriplet{
+		{
+			// extract single field from nested list
+			object: `{"listOfMaps":[{"name":"a","value":{"x":"1","y":"2"}},{"name":"b","value":{"z":"3"}}]}`,
+			set: _NS(
+				_P("listOfMaps", _KBF("name", "a"), "value", "x"),
+			),
+			wantOutput: typed.YAMLObject(`{"listOfMaps":[{"name":"a","value":{"x":"1"}}]}`),
+		},
+		{
+			// extract from deeply nested structure
+			object: `{"mapOfMapsRecursive":{"a":{"b":{"c":null,"d":{"e":null}}}}}`,
+			set: _NS(
+				_P("mapOfMapsRecursive", "a", "b", "c"),
+			),
+			wantOutput: typed.YAMLObject(`{"mapOfMapsRecursive":{"a":{"b":{"c":null}}}}`),
+		},
+	},
 }}
 
 func (tt extractWithKeysTestCase) test(t *testing.T) {