diff --git a/index.js b/index.js
index 3ebf3555c..d0c0de4f4 100755
--- a/index.js
+++ b/index.js
@@ -212,7 +212,7 @@ class NYC {
   }
 
   async instrumentAllFiles (input, output) {
-    let inputDir = '.' + path.sep
+    const inputDir = path.resolve(this.cwd, input)
     const visitor = async relFile => {
       const inFile = path.resolve(inputDir, relFile)
       const inCode = await fs.readFile(inFile, 'utf-8')
@@ -232,21 +232,19 @@ class NYC {
 
     this._loadAdditionalModules()
 
-    const stats = await fs.lstat(input)
+    const stats = await fs.lstat(inputDir)
     if (stats.isDirectory()) {
-      inputDir = input
-
-      const filesToInstrument = await this.exclude.glob(input)
+      const filesToInstrument = await this.exclude.glob(inputDir)
 
       const concurrency = output ? os.cpus().length : 1
       if (this.config.completeCopy && output) {
-        const files = await glob(path.resolve(input, '**'), {
+        const files = await glob(path.resolve(inputDir, '**'), {
           dot: true,
           nodir: true,
           ignore: ['**/.git', '**/.git/**', path.join(output, '**')]
         })
         const destDirs = new Set(
-          files.map(src => path.dirname(path.join(output, path.relative(input, src))))
+          files.map(src => path.dirname(path.join(output, path.relative(inputDir, src))))
         )
 
         await pMap(
@@ -256,14 +254,14 @@ class NYC {
         )
         await pMap(
           files,
-          src => fs.copyFile(src, path.join(output, path.relative(input, src))),
+          src => fs.copyFile(src, path.join(output, path.relative(inputDir, src))),
           { concurrency }
         )
       }
 
       await pMap(filesToInstrument, visitor, { concurrency })
     } else {
-      await visitor(input)
+      await visitor(inputDir)
     }
   }
 
@@ -294,7 +292,7 @@ class NYC {
 
     return (code, metadata, hash) => {
       const filename = metadata.filename
-      const sourceMap = this._getSourceMap(code, filename, hash)
+      const sourceMap = this._getSourceMap(code, path.resolve(this.cwd, filename), hash)
 
       try {
         instrumented = instrumenter.instrumentSync(code, filename, sourceMap)
diff --git a/lib/commands/instrument.js b/lib/commands/instrument.js
index cabb43775..cb350e115 100644
--- a/lib/commands/instrument.js
+++ b/lib/commands/instrument.js
@@ -24,6 +24,7 @@ exports.handler = cliWrapper(async argv => {
     throw new Error('cannot instrument files in place, <input> must differ from <output>.  Set \'--in-place\' to force')
   }
 
+  argv.cwd = path.resolve(argv.cwd)
   if (path.relative(argv.cwd, path.resolve(argv.cwd, argv.input)).startsWith('..')) {
     throw new Error('cannot instrument files outside project root directory')
   }
@@ -47,7 +48,7 @@ exports.handler = cliWrapper(async argv => {
     : './lib/instrumenters/noop'
 
   if (argv.inPlace) {
-    argv.output = argv.input
+    argv.output = path.join(argv.cwd, argv.input)
     argv.completeCopy = false
   }