Simple unit test showing kind of surprising behavior of Base64OutputStream. Basically, you *have* to call #close() on the OutputStream to get valid base64. After stumbling upon this I switched to Base64InputStream, because I can not close the Input/OutputStreams in my original code as I have to write additional non-base64 bytes into them too.

Base64OutputStreamTest.java

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;

import org.apache.commons.codec.binary.Base64InputStream;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.io.IOUtils;
import org.junit.Test;

public class Base64OutputStreamTest {
	final String original = "this is a message";
	final String originalAsBase64 = "dGhpcyBpcyBhIG1lc3NhZ2U=\r\n";

	@Test
	public void testBase64OutputStreamDoesNotConvertAllBytesIfNotClosed()
			throws IOException {
		ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
		OutputStream out = new Base64OutputStream(byteOut);
		out.write(original.getBytes());
		// in my original code, I can't close the stream here, because I need to
		// stream non-base64 bytes into it. All I can do is call #flush(), but
		// that does not write the missing bytes neither

		// why is this false?
		assertFalse(originalAsBase64.equals(byteOut.toString()));
	}

	@Test
	public void testBase64OutputStreamDoesConvertAllBytesIfClosed()
			throws IOException {
		ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
		OutputStream out = new Base64OutputStream(byteOut);
		out.write(original.getBytes());
		out.close();

		// calling out#close() does write the missing bytes and line delimiters
		assertEquals(originalAsBase64, byteOut.toString());
	}

	@Test
	public void testBase64InputStreamWorks() throws IOException {
		ByteArrayInputStream byteIn = new ByteArrayInputStream(
				originalAsBase64.getBytes());
		InputStream in = new Base64InputStream(byteIn, false);
		String result = IOUtils.toString(in);

		assertEquals(original, result);
	}

}