diff --git a/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/internal/CleanProperties.groovy b/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/internal/CleanProperties.groovy
new file mode 100644
index 000000000..f81b64a2b
--- /dev/null
+++ b/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/internal/CleanProperties.groovy
@@ -0,0 +1,32 @@
+/*
+ * Source https://stackoverflow.com/a/39043903/519333
+ */
+package com.github.jengelman.gradle.plugins.shadow.internal
+
+class CleanProperties extends Properties {
+    private static class StripFirstLineStream extends FilterOutputStream {
+
+        private boolean firstLineSeen = false
+
+        StripFirstLineStream(final OutputStream out) {
+            super(out)
+        }
+
+        @Override
+        void write(final int b) throws IOException {
+            if (firstLineSeen) {
+                super.write(b);
+            } else if (b == '\n') {
+                super.write(b);
+
+                firstLineSeen = true;
+            }
+        }
+
+    }
+
+    @Override
+    void store(final OutputStream out, final String comments) throws IOException {
+        super.store(new StripFirstLineStream(out), null)
+    }
+}
diff --git a/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformer.groovy b/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformer.groovy
index 31e1a5452..2d113ac2f 100644
--- a/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformer.groovy
+++ b/src/main/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformer.groovy
@@ -19,6 +19,7 @@
 
 package com.github.jengelman.gradle.plugins.shadow.transformers
 
+import com.github.jengelman.gradle.plugins.shadow.internal.CleanProperties
 import org.apache.tools.zip.ZipEntry
 import org.apache.tools.zip.ZipOutputStream
 import org.codehaus.plexus.util.IOUtil
@@ -117,7 +118,7 @@ import static groovy.lang.Closure.IDENTITY
 class PropertiesFileTransformer implements Transformer {
     private static final String PROPERTIES_SUFFIX = '.properties'
 
-    private Map<String, Properties> propertiesEntries = [:]
+    private Map<String, CleanProperties> propertiesEntries = [:]
 
     @Input
     List<String> paths = []
@@ -179,15 +180,17 @@ class PropertiesFileTransformer implements Transformer {
     }
 
     private Properties loadAndTransformKeys(InputStream is) {
-        Properties props = new Properties()
-        props.load(is)
+        Properties props = new CleanProperties()
+        if (is != null) {
+            props.load(is)
+        }
         return transformKeys(props)
     }
 
     private Properties transformKeys(Properties properties) {
         if (keyTransformer == IDENTITY)
             return properties
-        def result = new Properties()
+        def result = new CleanProperties()
         properties.each { key, value ->
             result.put(keyTransformer.call(key), value)
         }
diff --git a/src/test/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformerTest.groovy b/src/test/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformerTest.groovy
new file mode 100644
index 000000000..ff23aed96
--- /dev/null
+++ b/src/test/groovy/com/github/jengelman/gradle/plugins/shadow/transformers/PropertiesFileTransformerTest.groovy
@@ -0,0 +1,76 @@
+package com.github.jengelman.gradle.plugins.shadow.transformers
+
+import com.github.jengelman.gradle.plugins.shadow.ShadowStats
+import com.github.jengelman.gradle.plugins.shadow.relocation.Relocator
+import org.apache.tools.zip.ZipOutputStream
+import org.junit.Before
+import org.junit.Test
+
+import java.util.zip.ZipFile
+
+import static java.util.Arrays.asList
+import static org.junit.Assert.*
+
+/**
+ * Test for {@link PropertiesFileTransformer}.
+ */
+final class PropertiesFileTransformerTest extends TransformerTestSupport {
+    static final String MANIFEST_NAME = "META-INF/MANIFEST.MF"
+
+    private PropertiesFileTransformer transformer
+
+    @Before
+    void setUp() {
+        transformer = new PropertiesFileTransformer()
+    }
+
+    @Test
+    void testHasTransformedResource() {
+        transformer.transform(new TransformerContext(MANIFEST_NAME))
+
+        assertTrue(transformer.hasTransformedResource())
+    }
+
+    @Test
+    void testHasNotTransformedResource() {
+        assertFalse(transformer.hasTransformedResource())
+    }
+
+    @Test
+    void testTransformation() {
+        transformer.transform(new TransformerContext(MANIFEST_NAME, getResourceStream(MANIFEST_NAME), Collections.<Relocator>emptyList(), new ShadowStats()))
+
+        def testableZipFile = File.createTempFile("testable-zip-file-", ".jar")
+        def fileOutputStream = new FileOutputStream(testableZipFile)
+        def bufferedOutputStream = new BufferedOutputStream(fileOutputStream)
+        def zipOutputStream = new ZipOutputStream(bufferedOutputStream)
+
+        try {
+            transformer.modifyOutputStream(zipOutputStream, false)
+        } finally {
+            zipOutputStream.close()
+        }
+        def targetLines = readFrom(testableZipFile, MANIFEST_NAME)
+
+        assertFalse(targetLines.isEmpty())
+
+        assertTrue(targetLines.contains("Manifest-Version=1.0"))
+    }
+
+    static List<String> readFrom(File jarFile, String resourceName) {
+        def zip = new ZipFile(jarFile)
+        try {
+            def entry = zip.getEntry(resourceName)
+            if (!entry) {
+                return Collections.emptyList()
+            }
+            return zip.getInputStream(entry).readLines()
+        } finally {
+            zip.close()
+        }
+    }
+
+    InputStream getResourceStream(String resource) {
+        this.class.classLoader.getResourceAsStream(resource)
+    }
+}