diff --git a/package.json b/package.json
index b5336778..081fdf0d 100644
--- a/package.json
+++ b/package.json
@@ -49,6 +49,7 @@
   ],
   "dependencies": {
     "axe-core": "^2.3.1",
+    "env-paths": "^1.0.0",
     "express": "^4.15.5",
     "express-easy-zip": "^1.1.4",
     "extract-zip": "^1.6.5",
@@ -64,7 +65,7 @@
     "tmp": "0.0.31",
     "unzip": "^0.1.11",
     "uuidv4": "^0.5.0",
-    "winston": "^2.3.1",
+    "winston": "^2.4.0",
     "xmldom": "^0.1.27",
     "xpath": "^0.0.24"
   },
diff --git a/src/cli/cli.js b/src/cli/cli.js
index bf9fccda..c1044c5b 100755
--- a/src/cli/cli.js
+++ b/src/cli/cli.js
@@ -42,50 +42,63 @@ const cli = meow(`
   string: ['outdir', 'tempdir'],
 });
 
-logger.initLogger({verbose: cli.flags.verbose, silent: cli.flags.silent});
-
-// Check that an EPUB path is specified
-if (cli.input.length === 0) {
-  winston.error('Input required');
-  cli.showHelp(1);
+function sleep(ms) {
+  return new Promise(resolve => setTimeout(resolve, ms));
 }
 
-// Check that output directories can be overridden
-let outdir = cli.flags.outdir;
-if (outdir) {
-  if (cli.flags.subdir) {
-    outdir = path.join(outdir, path.parse(cli.input[0]).name);
+(async function processArgs() {
+  logger.initLogger({ verbose: cli.flags.verbose, silent: cli.flags.silent });
+
+  // Check that an EPUB path is specified
+  if (cli.input.length === 0) {
+    winston.logAndExit('error', 'Input required', () => {
+      console.log(cli.help);
+      process.exit(1);
+    });
+    await sleep(5000);
+    process.exit(1);
   }
-  if (!cli.flags.force) {
-    const overrides = ['ace.json', 'report.html', 'data', 'js']
-      .map(file => path.join(outdir, file))
-      .filter(fs.existsSync);
-    if (overrides.length > 0) {
-      winston.warn(`\
+
+  // Check that output directories can be overridden
+  let outdir = cli.flags.outdir;
+  if (outdir) {
+    if (cli.flags.subdir) {
+      outdir = path.join(outdir, path.parse(cli.input[0]).name);
+    }
+    if (!cli.flags.force) {
+      const overrides = ['ace.json', 'report.html', 'data', 'js']
+        .map(file => path.join(outdir, file))
+        .filter(fs.existsSync);
+      if (overrides.length > 0) {
+        winston.logAndExit('warn', `\
 Output directory is not empty.
 
-Running Ace would override the following files or directories:
+  Running Ace would override the following files or directories:
 
 ${overrides.map(file => `  - ${file}`).join('\n')}
 
-Use option --force to override.
-`);
-      process.exit(1);
+  Use option --force to override.
+  `, 1);
+        await sleep(5000);
+        process.exit(1);
+      }
     }
   }
-}
 
-// finally, invoke Ace
-ace(cli.input[0], {
-  cwd: cli.flags.cwd || process.cwd(),
-  outdir,
-  tmpdir: cli.flags.tempdir,
-  verbose: cli.flags.verbose,
-  silent: cli.flags.silent,
-  jobId: '',
-})
-.catch((err) => {
-  if (err) winston.error(err.message);
-  console.log(`Re-run Ace using the --verbose option to enable full debug logging.`)
-  process.exit(1);
-});
+  // finally, invoke Ace
+  ace(cli.input[0], {
+    cwd: cli.flags.cwd || process.cwd(),
+    outdir,
+    tmpdir: cli.flags.tempdir,
+    verbose: cli.flags.verbose,
+    silent: cli.flags.silent,
+    jobId: '',
+  })
+  .catch((err) => {
+    if (err && err.message) winston.error(err.message);
+    winston.logAndExit('info', 'Closing logs.', () => {
+      console.log('Re-run Ace using the --verbose option to enable full debug logging.');
+      process.exit(1);
+    });
+  });
+}());
diff --git a/src/core/logger.js b/src/core/logger.js
index d88addb0..38429bf2 100644
--- a/src/core/logger.js
+++ b/src/core/logger.js
@@ -1,29 +1,73 @@
 'use strict';
 
-const winston = require('winston');
+const envPaths = require('env-paths');
 const fs = require('fs-extra');
-const LOGFILE = __dirname + "/../ace.log";
+const path = require('path');
+const winston = require('winston');
 
-module.exports = {
-  initLogger: function(options) {
-    // clear old log file
-    fs.removeSync(LOGFILE);
+const acePaths = envPaths('DAISY Ace', { suffix: null });
 
-    // set up logger
-    var level = 'info';
-    if (options.verbose) {
-      level = 'verbose';
-    }
-    winston.configure({
-      level: level,
-      transports: [
-        new (winston.transports.File)({name: "file", filename: LOGFILE}),
-        new (winston.transports.Console)({name: "console"})
-      ]
+module.exports.initLogger = function initLogger(options = {}) {
+  // Check logging directoy exists
+  if (!fs.existsSync(acePaths.log)) {
+    fs.mkdirSync(acePaths.log);
+  }
+
+  // OS-dependant path to log file
+  const logfile = path.join(acePaths.log, 'ace.log');
+
+  // clear old log file
+  if (fs.existsSync(logfile)) {
+    fs.removeSync(logfile);
+  }
+
+  // set up logger
+  const level = (options.verbose) ? 'verbose' : 'info';
+  winston.configure({
+    level,
+    transports: [
+      new winston.transports.File({ name: 'file', filename: logfile }),
+      new winston.transports.Console({ name: 'console' }),
+    ],
+  });
+  if (options.silent) {
+    winston.remove('console');
+  }
+  winston.cli();
+};
+
+/* eslint-disable no-underscore-dangle */
+// Properly wait that loggers write to file before exitting
+// See https://github.com/winstonjs/winston/issues/228
+winston.logAndExit = function logAndExit(level, msg, codeOrCallback) {
+  const self = this;
+  this.log(level, msg, () => {
+    let numFlushes = 0;
+    let numFlushed = 0;
+    Object.keys(self.default.transports).forEach((k) => {
+      if (self.default.transports[k]._stream) {
+        numFlushes += 1;
+        self.default.transports[k]._stream.once('finish', () => {
+          numFlushed += 1;
+          if (numFlushes === numFlushed) {
+            if (typeof codeOrCallback === 'function') {
+              codeOrCallback();
+            } else {
+              process.exit(codeOrCallback);
+            }
+          }
+        });
+        self.default.transports[k]._stream.end();
+      }
     });
-    if (options.silent) {
-        winston.remove("console");
+    if (numFlushes === 0) {
+      if (typeof codeOrCallback === 'function') {
+        codeOrCallback();
+      } else {
+        process.exit(codeOrCallback);
+      }
     }
-    winston.cli();
-  }
-}
+  });
+};
+/* eslint-enable no-underscore-dangle */
+
diff --git a/tests/__tests__/__snapshots__/cli.test.js.snap b/tests/__tests__/__snapshots__/cli.test.js.snap
index 62167452..47b161fe 100644
--- a/tests/__tests__/__snapshots__/cli.test.js.snap
+++ b/tests/__tests__/__snapshots__/cli.test.js.snap
@@ -3,14 +3,14 @@
 exports[`test existing output 1`] = `
 "warn:    Output directory is not empty.
 
-Running Ace would override the following files or directories:
+  Running Ace would override the following files or directories:
 
   - report/ace.json
   - report/report.html
   - report/js
 
-Use option --force to override.
-
+  Use option --force to override.
+  
 "
 `;
 
@@ -64,7 +64,10 @@ exports[`test no input 2`] = `
 "
 `;
 
-exports[`test unexisting input 1`] = `"Re-run Ace using the --verbose option to enable full debug logging."`;
+exports[`test unexisting input 1`] = `
+"info:    Closing logs.
+Re-run Ace using the --verbose option to enable full debug logging."
+`;
 
 exports[`test unexisting input 2`] = `
 "error:   Couldn’t find EPUB file 'unexisting.epub'
diff --git a/yarn.lock b/yarn.lock
index 4960bc6a..c2df50fd 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1377,6 +1377,10 @@ enqueue@^1.0.2:
   dependencies:
     sliced "0.0.5"
 
+env-paths@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/env-paths/-/env-paths-1.0.0.tgz#4168133b42bb05c38a35b1ae4397c8298ab369e0"
+
 err-code@^1.0.0:
   version "1.1.2"
   resolved "https://registry.yarnpkg.com/err-code/-/err-code-1.1.2.tgz#06e0116d3028f6aef4806849eb0ea6a748ae6960"
@@ -4565,9 +4569,9 @@ window-size@0.1.0:
   version "0.1.0"
   resolved "https://registry.yarnpkg.com/window-size/-/window-size-0.1.0.tgz#5438cd2ea93b202efa3a19fe8887aee7c94f9c9d"
 
-winston@^2.3.1:
-  version "2.3.1"
-  resolved "https://registry.yarnpkg.com/winston/-/winston-2.3.1.tgz#0b48420d978c01804cf0230b648861598225a119"
+winston@^2.4.0:
+  version "2.4.0"
+  resolved "https://registry.yarnpkg.com/winston/-/winston-2.4.0.tgz#808050b93d52661ed9fb6c26b3f0c826708b0aee"
   dependencies:
     async "~1.0.0"
     colors "1.0.x"