You can use DOM to chain transforms in memory.

Example:

// Setup the transformations
Transformation tfactory = TransformerFactory.newInstance();
Transformer step1xform = tfactory.newTransformer(new StreamSource("step1.xsl"));
Transformer step2xform = tfactory.newTransformer(new StreamSource("step2.xsl"));

// Create a DOMResult to hold the between XML document
DOMResult between = new DOMResult();

// Transform the input
step1xform.transform(new StreamSource("in.xml"),between);

// Transform the output of step 1
step2xform.transform(new DOMSource(between.getNode()),new StreamResult("out.xml"));