diff --git a/discovery/file/file.go b/discovery/file/file.go
index 911d87039..adb71127c 100644
--- a/discovery/file/file.go
+++ b/discovery/file/file.go
@@ -22,6 +22,7 @@ import (
 	"os"
 	"path/filepath"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/go-kit/kit/log"
@@ -38,10 +39,9 @@ const fileSDFilepathLabel = model.MetaLabelPrefix + "filepath"
 
 // TimestampCollector is a Custom Collector for Timestamps of the files.
 type TimestampCollector struct {
-	filenames   []string
 	Description *prometheus.Desc
-
-	logger log.Logger
+	discoverers map[*Discovery]struct{}
+	lock        sync.RWMutex
 }
 
 // Describe method sends the description to the channel.
@@ -49,38 +49,49 @@ func (t *TimestampCollector) Describe(ch chan<- *prometheus.Desc) {
 	ch <- t.Description
 }
 
-// SetFiles changes the filenames of the struct to the paths returned by listfiles().
-func (t *TimestampCollector) SetFiles(files []string) {
-	t.filenames = files
-}
-
 // Collect creates constant metrics for each file with last modified time of the file.
 func (t *TimestampCollector) Collect(ch chan<- prometheus.Metric) {
-	files := t.filenames
-	for i := 0; i < len(files); i++ {
-		info, err := os.Stat(files[i])
-		if err != nil {
-			t.logger.Errorf("Error getting the fileinfo of the file %q: %s", files[i], err)
-			continue
+	// New map to dedup filenames.
+	uniqueFiles := make(map[string]float64)
+	t.lock.RLock()
+	for fileSD := range t.discoverers {
+		for filename, timestamp := range fileSD.timestamps {
+			uniqueFiles[filename] = timestamp
 		}
+	}
+	t.lock.RUnlock()
+	for filename, timestamp := range uniqueFiles {
 		ch <- prometheus.MustNewConstMetric(
 			t.Description,
 			prometheus.GaugeValue,
-			float64(info.ModTime().Unix()),
-			files[i],
+			timestamp,
+			filename,
 		)
 	}
 }
 
+func (t *TimestampCollector) addDiscoverer(disc *Discovery) {
+	t.lock.Lock()
+	t.discoverers[disc] = struct{}{}
+	t.lock.Unlock()
+}
+
+func (t *TimestampCollector) removeDiscoverer(disc *Discovery) {
+	t.lock.Lock()
+	delete(t.discoverers, disc)
+	t.lock.Unlock()
+}
+
 // NewTimestampCollector creates a TimestampCollector.
 func NewTimestampCollector() *TimestampCollector {
 	return &TimestampCollector{
 		Description: prometheus.NewDesc(
 			"prometheus_sd_file_timestamp",
-			"Timestamp of files read by FileSD",
+			"Timestamp (mtime) of files read by FileSD. Timestamp is set at read time.",
 			[]string{"filename"},
 			nil,
 		),
+		discoverers: make(map[*Discovery]struct{}),
 	}
 }
 
@@ -108,9 +119,11 @@ func init() {
 // on files that contain target groups in JSON or YAML format. Refreshing
 // happens using file watches and periodic refreshes.
 type Discovery struct {
-	paths    []string
-	watcher  *fsnotify.Watcher
-	interval time.Duration
+	paths      []string
+	watcher    *fsnotify.Watcher
+	interval   time.Duration
+	timestamps map[string]float64
+	lock       sync.RWMutex
 
 	// lastRefresh stores which files were found during the last refresh
 	// and how many target groups they contained.
@@ -124,11 +137,15 @@ func NewDiscovery(conf *config.FileSDConfig, logger log.Logger) *Discovery {
 	if logger == nil {
 		logger = log.NewNopLogger()
 	}
-	return &Discovery{
-		paths:    conf.Files,
-		interval: time.Duration(conf.RefreshInterval),
-		logger:   logger,
+
+	disc := &Discovery{
+		paths:      conf.Files,
+		interval:   time.Duration(conf.RefreshInterval),
+		timestamps: make(map[string]float64),
+		logger:     logger,
 	}
+	fileSDTimeStamp.addDiscoverer(disc)
+	return disc
 }
 
 // listFiles returns a list of all files that match the configured patterns.
@@ -212,6 +229,18 @@ func (d *Discovery) Run(ctx context.Context, ch chan<- []*config.TargetGroup) {
 	}
 }
 
+func (d *Discovery) writeTimestamp(filename string, timestamp float64) {
+	d.lock.Lock()
+	d.timestamps[filename] = timestamp
+	d.lock.Unlock()
+}
+
+func (d *Discovery) deleteTimestamp(filename string) {
+	d.lock.Lock()
+	delete(d.timestamps, filename)
+	d.lock.Unlock()
+}
+
 // stop shuts down the file watcher.
 func (d *Discovery) stop() {
 	level.Debug(d.logger).Log("msg", "Stopping file discovery...", "paths", d.paths)
@@ -219,6 +248,8 @@ func (d *Discovery) stop() {
 	done := make(chan struct{})
 	defer close(done)
 
+	fileSDTimeStamp.removeDiscoverer(d)
+
 	// Closing the watcher will deadlock unless all events and errors are drained.
 	go func() {
 		for {
@@ -245,11 +276,9 @@ func (d *Discovery) refresh(ctx context.Context, ch chan<- []*config.TargetGroup
 	defer func() {
 		fileSDScanDuration.Observe(time.Since(t0).Seconds())
 	}()
-
-	fileSDTimeStamp.SetFiles(d.listFiles())
 	ref := map[string]int{}
 	for _, p := range d.listFiles() {
-		tgroups, err := readFile(p)
+		tgroups, err := d.readFile(p)
 		if err != nil {
 			fileSDReadErrorsCount.Inc()
 
@@ -270,6 +299,8 @@ func (d *Discovery) refresh(ctx context.Context, ch chan<- []*config.TargetGroup
 	for f, n := range d.lastRefresh {
 		m, ok := ref[f]
 		if !ok || n > m {
+			level.Debug(d.logger).Log("msg", "file_sd refresh found file that should be removed", "file", f)
+			d.deleteTimestamp(f)
 			for i := m; i < n; i++ {
 				select {
 				case ch <- []*config.TargetGroup{{Source: fileSource(f, i)}}:
@@ -284,15 +315,21 @@ func (d *Discovery) refresh(ctx context.Context, ch chan<- []*config.TargetGroup
 	d.watchFiles()
 }
 
-// fileSource returns a source ID for the i-th target group in the file.
-func fileSource(filename string, i int) string {
-	return fmt.Sprintf("%s:%d", filename, i)
-}
-
 // readFile reads a JSON or YAML list of targets groups from the file, depending on its
 // file extension. It returns full configuration target groups.
-func readFile(filename string) ([]*config.TargetGroup, error) {
-	content, err := ioutil.ReadFile(filename)
+func (d *Discovery) readFile(filename string) ([]*config.TargetGroup, error) {
+	fd, err := os.Open(filename)
+	if err != nil {
+		return nil, err
+	}
+	defer fd.Close()
+
+	content, err := ioutil.ReadAll(fd)
+	if err != nil {
+		return nil, err
+	}
+
+	info, err := fd.Stat()
 	if err != nil {
 		return nil, err
 	}
@@ -324,5 +361,13 @@ func readFile(filename string) ([]*config.TargetGroup, error) {
 		}
 		tg.Labels[fileSDFilepathLabel] = model.LabelValue(filename)
 	}
+
+	d.writeTimestamp(filename, float64(info.ModTime().Unix()))
+
 	return targetGroups, nil
 }
+
+// fileSource returns a source ID for the i-th target group in the file.
+func fileSource(filename string, i int) string {
+	return fmt.Sprintf("%s:%d", filename, i)
+}