diff --git a/bin/generate.js b/bin/generate.js
index 3fd372b2..d3f65017 100755
--- a/bin/generate.js
+++ b/bin/generate.js
@@ -57,6 +57,9 @@ if (args.h || args.help || args._.length > 1) {
     const baseURL = args.b || 'https://query.linkeddatafragments.org/';
     const webpackConfig = require(args.w ? path.resolve(process.cwd(), args.w) : '../webpack.config.js');
 
+    // Remove the location of queries.json which shouldn't be present in the build configuration.
+    webpackConfig[0].entry=webpackConfig[0].entry.filter(x => !x.endsWith('queries.json'));
+
     // Override the baseURL in the webpack config
     webpackConfig.baseURL.replace = baseURL;
 
@@ -66,6 +69,7 @@ if (args.h || args.help || args._.length > 1) {
             entry.output.path = path.resolve(process.cwd(), destinationPath);
         }
     }
+
     webpack(webpackConfig, (err, stats) => {
         if (err) {
             console.error(err.stack || err);
@@ -82,4 +86,12 @@ if (args.h || args.help || args._.length > 1) {
 
         fs.unlinkSync('.tmp-comunica-engine.js');
     });
+
+    if (fs.existsSync(path.join(process.cwd(), 'queries.json'))) {
+        // Create the build output folder if it doesn't exist
+        if (! fs.existsSync(path.resolve(process.cwd(), destinationPath))) {
+            fs.mkdirSync(path.resolve(process.cwd(), destinationPath));
+        }
+        fs.renameSync(path.join(process.cwd(), 'queries.json'), path.resolve(process.cwd(), `${destinationPath}/queries.json`));
+    };
 })();