diff --git a/jsdoc.js b/jsdoc.js
index beaf2b22..28ceca8a 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -155,10 +155,6 @@ function main() {
         throw('Configuration file cannot be evaluated. '+e);
     }
     
-    if (env.opts.query) {
-        env.opts.query = require('query').toObject(env.opts.query);
-    }
-    
     // allow to pass arguments from configuration file
     if (env.conf.opts) {
         for (var opt in env.conf.opts) {
@@ -169,6 +165,10 @@ function main() {
         }
     }
     
+    if (env.opts.query) {
+        env.opts.query = require('query').toObject(env.opts.query);
+    }
+    
     // which version of javascript will be supported? (rhino only)
     if (typeof version === 'function') {
         version(env.conf.jsVersion || 180);