diff --git a/modules/lang-mustache/src/test/java/org/elasticsearch/script/mustache/SearchTemplateIT.java b/modules/lang-mustache/src/test/java/org/elasticsearch/script/mustache/SearchTemplateIT.java
index fe2fedf62b5..884e26e7df8 100644
--- a/modules/lang-mustache/src/test/java/org/elasticsearch/script/mustache/SearchTemplateIT.java
+++ b/modules/lang-mustache/src/test/java/org/elasticsearch/script/mustache/SearchTemplateIT.java
@@ -198,6 +198,7 @@ public class SearchTemplateIT extends ESSingleNodeTestCase {
 
         getResponse = client().admin().cluster().prepareGetStoredScript("testTemplate").get();
         assertNull(getResponse.getSource());
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
     }
 
     public void testIndexedTemplate() throws Exception {
@@ -267,6 +268,7 @@ public class SearchTemplateIT extends ESSingleNodeTestCase {
                 .setScript("2").setScriptType(ScriptType.STORED).setScriptParams(templateParams)
                 .get();
         assertHitCount(searchResponse.getResponse(), 1);
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
     }
 
     // Relates to #10397
@@ -311,6 +313,7 @@ public class SearchTemplateIT extends ESSingleNodeTestCase {
                     .get();
             assertHitCount(searchResponse.getResponse(), 1);
         }
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
     }
 
     public void testIndexedTemplateWithArray() throws Exception {
@@ -339,6 +342,7 @@ public class SearchTemplateIT extends ESSingleNodeTestCase {
                 .setScript("4").setScriptType(ScriptType.STORED).setScriptParams(arrayTemplateParams)
                 .get();
         assertHitCount(searchResponse.getResponse(), 5);
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
     }
 
 }
diff --git a/server/src/main/java/org/elasticsearch/script/StoredScriptSource.java b/server/src/main/java/org/elasticsearch/script/StoredScriptSource.java
index da6dad1dff3..11f8769c86b 100644
--- a/server/src/main/java/org/elasticsearch/script/StoredScriptSource.java
+++ b/server/src/main/java/org/elasticsearch/script/StoredScriptSource.java
@@ -74,6 +74,11 @@ public class StoredScriptSource extends AbstractDiffable<StoredScriptSource> imp
      */
     public static final ParseField TEMPLATE_PARSE_FIELD = new ParseField("template");
 
+    /**
+     * Standard {@link ParseField} for query on the inner field.
+     */
+    public static final ParseField TEMPLATE_NO_WRAPPER_PARSE_FIELD = new ParseField("query");
+
     /**
      * Standard {@link ParseField} for lang on the inner level.
      */
@@ -189,6 +194,26 @@ public class StoredScriptSource extends AbstractDiffable<StoredScriptSource> imp
         PARSER.declareField(Builder::setOptions, XContentParser::mapStrings, OPTIONS_PARSE_FIELD, ValueType.OBJECT);
     }
 
+    private static StoredScriptSource parseRemaining(Token token, XContentParser parser) throws IOException {
+        try (XContentBuilder builder = XContentFactory.jsonBuilder()) {
+            if (token != Token.START_OBJECT) {
+                builder.startObject();
+                builder.copyCurrentStructure(parser);
+                builder.endObject();
+            } else {
+                builder.copyCurrentStructure(parser);
+            }
+
+            String source = Strings.toString(builder);
+
+            if (source == null || source.isEmpty()) {
+                DEPRECATION_LOGGER.deprecated("empty templates should no longer be used");
+            }
+
+            return new StoredScriptSource(Script.DEFAULT_TEMPLATE_LANG, source, Collections.emptyMap());
+        }
+    }
+
     /**
      * This will parse XContent into a {@link StoredScriptSource}.  The following formats can be parsed:
      *
@@ -304,38 +329,28 @@ public class StoredScriptSource extends AbstractDiffable<StoredScriptSource> imp
                 } else {
                     throw new ParsingException(parser.getTokenLocation(), "unexpected token [" + token + "], expected [{, <source>]");
                 }
-            } else {
-                if (TEMPLATE_PARSE_FIELD.getPreferredName().equals(name)) {
-                    token = parser.nextToken();
+            } else if (TEMPLATE_PARSE_FIELD.getPreferredName().equals(name)) {
 
-                    if (token == Token.VALUE_STRING) {
-                        String source = parser.text();
+                DEPRECATION_LOGGER.deprecated("the template context is now deprecated. Specify templates in a \"script\" element.");
 
-                        if (source == null || source.isEmpty()) {
-                            DEPRECATION_LOGGER.deprecated("empty templates should no longer be used");
-                        }
-
-                        return new StoredScriptSource(Script.DEFAULT_TEMPLATE_LANG, source, Collections.emptyMap());
-                    }
-                }
-
-                try (XContentBuilder builder = XContentFactory.jsonBuilder()) {
-                    if (token != Token.START_OBJECT) {
-                        builder.startObject();
-                        builder.copyCurrentStructure(parser);
-                        builder.endObject();
-                    } else {
-                        builder.copyCurrentStructure(parser);
-                    }
-
-                    String source = Strings.toString(builder);
+                token = parser.nextToken();
+                if (token == Token.VALUE_STRING) {
+                    String source = parser.text();
 
                     if (source == null || source.isEmpty()) {
                         DEPRECATION_LOGGER.deprecated("empty templates should no longer be used");
                     }
 
                     return new StoredScriptSource(Script.DEFAULT_TEMPLATE_LANG, source, Collections.emptyMap());
+                } else {
+                    return parseRemaining(token, parser);
                 }
+            } else if (TEMPLATE_NO_WRAPPER_PARSE_FIELD.getPreferredName().equals(name)) {
+                DEPRECATION_LOGGER.deprecated("the template context is now deprecated. Specify templates in a \"script\" element.");
+                return parseRemaining(token, parser);
+            } else {
+                DEPRECATION_LOGGER.deprecated("scripts should not be stored without a context. Specify them in a \"script\" element.");
+                return parseRemaining(token, parser);
             }
         } catch (IOException ioe) {
             throw new UncheckedIOException(ioe);
diff --git a/server/src/test/java/org/elasticsearch/script/ScriptMetaDataTests.java b/server/src/test/java/org/elasticsearch/script/ScriptMetaDataTests.java
index 32d4d48a448..bef20190acf 100644
--- a/server/src/test/java/org/elasticsearch/script/ScriptMetaDataTests.java
+++ b/server/src/test/java/org/elasticsearch/script/ScriptMetaDataTests.java
@@ -81,10 +81,12 @@ public class ScriptMetaDataTests extends AbstractSerializingTestCase<ScriptMetaD
         XContentBuilder sourceBuilder = XContentFactory.jsonBuilder();
         sourceBuilder.startObject().startObject("template").field("field", "value").endObject().endObject();
         builder.storeScript("template", StoredScriptSource.parse(BytesReference.bytes(sourceBuilder), sourceBuilder.contentType()));
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
 
         sourceBuilder = XContentFactory.jsonBuilder();
         sourceBuilder.startObject().field("template", "value").endObject();
         builder.storeScript("template_field", StoredScriptSource.parse(BytesReference.bytes(sourceBuilder), sourceBuilder.contentType()));
+        assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
 
         sourceBuilder = XContentFactory.jsonBuilder();
         sourceBuilder.startObject().startObject("script").field("lang", "_lang").field("source", "_source").endObject().endObject();
@@ -99,14 +101,19 @@ public class ScriptMetaDataTests extends AbstractSerializingTestCase<ScriptMetaD
     public void testDiff() throws Exception {
         ScriptMetaData.Builder builder = new ScriptMetaData.Builder(null);
         builder.storeScript("1", StoredScriptSource.parse(new BytesArray("{\"foo\":\"abc\"}"), XContentType.JSON));
+        assertWarnings("scripts should not be stored without a context. Specify them in a \"script\" element.");
         builder.storeScript("2", StoredScriptSource.parse(new BytesArray("{\"foo\":\"def\"}"), XContentType.JSON));
+        assertWarnings("scripts should not be stored without a context. Specify them in a \"script\" element.");
         builder.storeScript("3", StoredScriptSource.parse(new BytesArray("{\"foo\":\"ghi\"}"), XContentType.JSON));
+        assertWarnings("scripts should not be stored without a context. Specify them in a \"script\" element.");
         ScriptMetaData scriptMetaData1 = builder.build();
 
         builder = new ScriptMetaData.Builder(scriptMetaData1);
         builder.storeScript("2", StoredScriptSource.parse(new BytesArray("{\"foo\":\"changed\"}"), XContentType.JSON));
+        assertWarnings("scripts should not be stored without a context. Specify them in a \"script\" element.");
         builder.deleteScript("3");
         builder.storeScript("4", StoredScriptSource.parse(new BytesArray("{\"foo\":\"jkl\"}"), XContentType.JSON));
+        assertWarnings("scripts should not be stored without a context. Specify them in a \"script\" element.");
         ScriptMetaData scriptMetaData2 = builder.build();
 
         ScriptMetaData.ScriptMetadataDiff diff = (ScriptMetaData.ScriptMetadataDiff) scriptMetaData2.diff(scriptMetaData1);
diff --git a/server/src/test/java/org/elasticsearch/script/StoredScriptSourceTests.java b/server/src/test/java/org/elasticsearch/script/StoredScriptSourceTests.java
index 8aa4ca57acf..49e26236268 100644
--- a/server/src/test/java/org/elasticsearch/script/StoredScriptSourceTests.java
+++ b/server/src/test/java/org/elasticsearch/script/StoredScriptSourceTests.java
@@ -50,7 +50,9 @@ public class StoredScriptSourceTests extends AbstractSerializingTestCase<StoredS
             if (randomBoolean()) {
                 options.put(Script.CONTENT_TYPE_OPTION, xContentType.mediaType());
             }
-            return StoredScriptSource.parse(BytesReference.bytes(template), xContentType);
+            StoredScriptSource source = StoredScriptSource.parse(BytesReference.bytes(template), xContentType);
+            assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
+            return source;
         } catch (IOException e) {
             throw new AssertionError("Failed to create test instance", e);
         }
diff --git a/server/src/test/java/org/elasticsearch/script/StoredScriptTests.java b/server/src/test/java/org/elasticsearch/script/StoredScriptTests.java
index 79e3195f3d9..04483c869d9 100644
--- a/server/src/test/java/org/elasticsearch/script/StoredScriptTests.java
+++ b/server/src/test/java/org/elasticsearch/script/StoredScriptTests.java
@@ -74,6 +74,7 @@ public class StoredScriptTests extends AbstractSerializingTestCase<StoredScriptS
             StoredScriptSource source = new StoredScriptSource("mustache", "code", Collections.emptyMap());
 
             assertThat(parsed, equalTo(source));
+            assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
         }
 
         // complex template with wrapper template object
@@ -89,6 +90,7 @@ public class StoredScriptTests extends AbstractSerializingTestCase<StoredScriptS
             StoredScriptSource source = new StoredScriptSource("mustache", code, Collections.emptyMap());
 
             assertThat(parsed, equalTo(source));
+            assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
         }
 
         // complex template with no wrapper object
@@ -104,6 +106,7 @@ public class StoredScriptTests extends AbstractSerializingTestCase<StoredScriptS
             StoredScriptSource source = new StoredScriptSource("mustache", code, Collections.emptyMap());
 
             assertThat(parsed, equalTo(source));
+            assertWarnings("the template context is now deprecated. Specify templates in a \"script\" element.");
         }
 
         // complex template using script as the field name
@@ -223,7 +226,10 @@ public class StoredScriptTests extends AbstractSerializingTestCase<StoredScriptS
             StoredScriptSource source = new StoredScriptSource(Script.DEFAULT_TEMPLATE_LANG, "", Collections.emptyMap());
 
             assertThat(parsed, equalTo(source));
-            assertWarnings("empty templates should no longer be used");
+            assertWarnings(
+                "the template context is now deprecated. Specify templates in a \"script\" element.",
+                "empty templates should no longer be used"
+            );
         }
 
         try (XContentBuilder builder = XContentFactory.contentBuilder(XContentType.JSON)) {