diff --git a/hibernate-core/src/main/java/org/hibernate/jpa/boot/internal/EntityManagerFactoryBuilderImpl.java b/hibernate-core/src/main/java/org/hibernate/jpa/boot/internal/EntityManagerFactoryBuilderImpl.java
index 55e7ed2cae..94e1dea153 100644
--- a/hibernate-core/src/main/java/org/hibernate/jpa/boot/internal/EntityManagerFactoryBuilderImpl.java
+++ b/hibernate-core/src/main/java/org/hibernate/jpa/boot/internal/EntityManagerFactoryBuilderImpl.java
@@ -471,17 +471,14 @@ public class EntityManagerFactoryBuilderImpl implements EntityManagerFactoryBuil
 		final ConfigLoader configLoader = new ConfigLoader( ssrBuilder.getBootstrapServiceRegistry() );
 
 		// see if the persistence.xml settings named a Hibernate config file....
-		final String cfgXmlResourceName1 = (String) mergedSettings.configurationValues.remove( CFG_FILE );
-		if ( StringHelper.isNotEmpty( cfgXmlResourceName1 ) ) {
-			final LoadedConfig loadedCfg = configLoader.loadConfigXmlResource( cfgXmlResourceName1 );
-			processConfigXml( loadedCfg, mergedSettings, ssrBuilder );
+		String cfgXmlResourceName = (String) mergedSettings.configurationValues.remove( CFG_FILE );
+		if ( StringHelper.isEmpty( cfgXmlResourceName ) ) {
+			// see if integration settings named a Hibernate config file....
+			cfgXmlResourceName = (String) integrationSettings.get( CFG_FILE );
 		}
 
-		// see if integration settings named a Hibernate config file....
-		final String cfgXmlResourceName2 = (String) integrationSettings.get( CFG_FILE );
-		if ( StringHelper.isNotEmpty( cfgXmlResourceName2 ) ) {
-			integrationSettings.remove( CFG_FILE );
-			final LoadedConfig loadedCfg = configLoader.loadConfigXmlResource( cfgXmlResourceName2 );
+		if ( StringHelper.isNotEmpty( cfgXmlResourceName ) ) {
+			final LoadedConfig loadedCfg = configLoader.loadConfigXmlResource( cfgXmlResourceName );
 			processConfigXml( loadedCfg, mergedSettings, ssrBuilder );
 		}
 
diff --git a/hibernate-core/src/test/java/org/hibernate/cfg/CfgFilePropertyTest.java b/hibernate-core/src/test/java/org/hibernate/cfg/CfgFilePropertyTest.java
new file mode 100644
index 0000000000..a58fd2e10b
--- /dev/null
+++ b/hibernate-core/src/test/java/org/hibernate/cfg/CfgFilePropertyTest.java
@@ -0,0 +1,66 @@
+/*
+ * Hibernate, Relational Persistence for Idiomatic Java
+ *
+ * License: GNU Lesser General Public License (LGPL), version 2.1 or later.
+ * See the lgpl.txt file in the root directory or <http://www.gnu.org/licenses/lgpl-2.1.html>.
+ */
+package org.hibernate.cfg;
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Properties;
+import java.util.concurrent.atomic.AtomicReference;
+import javax.persistence.Persistence;
+
+import org.hibernate.testing.TestForIssue;
+import org.hibernate.testing.junit4.BaseUnitTestCase;
+import org.junit.Test;
+
+import static org.hibernate.internal.util.ConfigHelper.findAsResource;
+import static org.junit.Assert.assertNull;
+
+/**
+ * @author Vlad Mihalcea
+ */
+@TestForIssue(jiraKey = "HHH-13227")
+public class CfgFilePropertyTest extends BaseUnitTestCase {
+
+	@Test
+	public void test() throws InterruptedException {
+
+		final AtomicReference<Exception> exceptionHolder = new AtomicReference<>();
+
+		Thread thread = new Thread( () -> {
+			try {
+				final Properties props = new Properties();
+				props.setProperty( AvailableSettings.CFG_FILE, "/org/hibernate/test/boot/cfgXml/hibernate.cfg.xml" );
+
+				Persistence.createEntityManagerFactory( "ExcludeUnlistedClassesTest1", props );
+			}
+			catch (Exception e) {
+				exceptionHolder.set( e );
+			}
+		} );
+		thread.setContextClassLoader( new ClassLoader() {
+
+			@Override
+			protected Enumeration<URL> findResources(String name) throws IOException {
+				return name.equals( "META-INF/persistence.xml" ) ?
+					Collections.enumeration(
+						Collections.singletonList(
+							findAsResource( "org/hibernate/jpa/test/persistenceunit/META-INF/persistence.xml" )
+						)
+					) :
+					Collections.emptyEnumeration();
+			}
+		}  );
+
+		thread.start();
+		thread.join();
+
+		assertNull( exceptionHolder.get() );
+	}
+}