diff --git a/src/main/java/org/scijava/annotations/AnnotationProcessor.java b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
index 778d909fa..fe0a5c26b 100644
--- a/src/main/java/org/scijava/annotations/AnnotationProcessor.java
+++ b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
@@ -32,7 +32,9 @@
 package org.scijava.annotations;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -62,6 +64,7 @@
 import javax.lang.model.util.Elements;
 import javax.lang.model.util.Types;
 import javax.tools.Diagnostic.Kind;
+import javax.tools.FileObject;
 import javax.tools.StandardLocation;
 
 import org.scijava.annotations.AbstractIndexWriter.StreamFactory;
@@ -90,14 +93,14 @@ public boolean process(final Set<? extends TypeElement> elements,
 		try {
 			writer.write(writer);
 		}
-		catch (IOException e) {
+		catch (final IOException e) {
 			final ByteArrayOutputStream out = new ByteArrayOutputStream();
 			e.printStackTrace(new PrintStream(out));
 			try {
 				out.close();
 				processingEnv.getMessager().printMessage(Kind.ERROR, out.toString());
 			}
-			catch (IOException e2) {
+			catch (final IOException e2) {
 				processingEnv.getMessager().printMessage(Kind.ERROR,
 					e2.getMessage() + " while printing " + e.getMessage());
 			}
@@ -152,8 +155,9 @@ public void add(final TypeElement element) {
 		}
 
 		@SuppressWarnings("unchecked")
-		private Map<String, Object> adapt(List<? extends AnnotationMirror> mirrors,
-			TypeMirror annotationType)
+		private Map<String, Object> adapt(
+			final List<? extends AnnotationMirror> mirrors,
+			final TypeMirror annotationType)
 		{
 			final Map<String, Object> result = new TreeMap<String, Object>();
 			for (final AnnotationMirror mirror : mirrors) {
@@ -208,7 +212,8 @@ else if (o instanceof VariableElement) {
 		}
 
 		private AnnotationMirror getMirror(final TypeElement element) {
-			for (AnnotationMirror candidate : utils.getAllAnnotationMirrors(element))
+			for (final AnnotationMirror candidate : utils
+				.getAllAnnotationMirrors(element))
 			{
 				final Name binaryName =
 					utils.getBinaryName((TypeElement) candidate.getAnnotationType()
@@ -221,7 +226,9 @@ private AnnotationMirror getMirror(final TypeElement element) {
 		}
 
 		@Override
-		public InputStream openInput(String annotationName) throws IOException {
+		public InputStream openInput(final String annotationName)
+			throws IOException
+		{
 			try {
 				return filer.getResource(StandardLocation.CLASS_OUTPUT, "",
 					Index.INDEX_PREFIX + annotationName).openInputStream();
@@ -232,16 +239,37 @@ public InputStream openInput(String annotationName) throws IOException {
 		}
 
 		@Override
-		public OutputStream openOutput(String annotationName) throws IOException {
+		public OutputStream openOutput(final String annotationName)
+			throws IOException
+		{
 			final List<Element> originating = originatingElements.get(annotationName);
-			return filer.createResource(StandardLocation.CLASS_OUTPUT, "",
-				Index.INDEX_PREFIX + annotationName,
-				originating.toArray(new Element[originating.size()]))
-				.openOutputStream();
+			final String path = Index.INDEX_PREFIX + annotationName;
+			final FileObject fileObject =
+				filer.createResource(StandardLocation.CLASS_OUTPUT, "", path,
+					originating.toArray(new Element[originating.size()]));
+
+			/*
+			 * Verify that the generated file is in the META-INF/json/ subdirectory;
+			 * Despite our asking for it explicitly, the DefaultFileManager will
+			 * strip out the directory if javac was called without an explicit
+			 * output directory (i.e. without <code>-d</code> option).
+			 */
+			final String uri = fileObject.toUri().toString();
+			if (uri != null && uri.endsWith("/" + path)) {
+				return fileObject.openOutputStream();
+			}
+			final String prefix =
+				uri.substring(0, uri.length() - annotationName.length());
+			final File file = new File(prefix + path);
+			final File parent = file.getParentFile();
+			if (parent != null && !parent.isDirectory() && !parent.mkdirs()) {
+				throw new IOException("Could not create directory: " + parent);
+			}
+			return new FileOutputStream(file);
 		}
 
 		@Override
-		public boolean isClassObsolete(String className) {
+		public boolean isClassObsolete(final String className) {
 			return false;
 		}