diff --git a/cmd/fs-v1-multipart.go b/cmd/fs-v1-multipart.go
index 6bdc5bb42..8d59338a7 100644
--- a/cmd/fs-v1-multipart.go
+++ b/cmd/fs-v1-multipart.go
@@ -24,6 +24,7 @@ import (
 	"fmt"
 	"io/ioutil"
 	"os"
+	"path/filepath"
 	"sort"
 	"strconv"
 	"strings"
@@ -35,6 +36,11 @@ import (
 	"github.com/minio/pkg/trie"
 )
 
+const (
+	bgAppendsDirName         = "bg-appends"
+	bgAppendsCleanupInterval = 10 * time.Minute
+)
+
 // Returns EXPORT/.minio.sys/multipart/SHA256/UPLOADID
 func (fs *FSObjects) getUploadIDDir(bucket, object, uploadID string) string {
 	return pathJoin(fs.fsPath, minioMetaMultipartBucket, getSHA256Hash([]byte(pathJoin(bucket, object))), uploadID)
@@ -74,7 +80,7 @@ func (fs *FSObjects) backgroundAppend(ctx context.Context, bucket, object, uploa
 	file := fs.appendFileMap[uploadID]
 	if file == nil {
 		file = &fsAppendFile{
-			filePath: pathJoin(fs.fsPath, minioMetaTmpBucket, fs.fsUUID, fmt.Sprintf("%s.%s", uploadID, mustGetUUID())),
+			filePath: pathJoin(fs.fsPath, minioMetaTmpBucket, fs.fsUUID, bgAppendsDirName, fmt.Sprintf("%s.%s", uploadID, mustGetUUID())),
 		}
 		fs.appendFileMap[uploadID] = file
 	}
@@ -643,7 +649,7 @@ func (fs *FSObjects) CompleteMultipartUpload(ctx context.Context, bucket string,
 	}
 
 	appendFallback := true // In case background-append did not append the required parts.
-	appendFilePath := pathJoin(fs.fsPath, minioMetaTmpBucket, fs.fsUUID, fmt.Sprintf("%s.%s", uploadID, mustGetUUID()))
+	appendFilePath := pathJoin(fs.fsPath, minioMetaTmpBucket, fs.fsUUID, "bg-appends", fmt.Sprintf("%s.%s", uploadID, mustGetUUID()))
 
 	// Most of the times appendFile would already be fully appended by now. We call fs.backgroundAppend()
 	// to take care of the following corner case:
@@ -843,58 +849,99 @@ func (fs *FSObjects) AbortMultipartUpload(ctx context.Context, bucket, object, u
 	return nil
 }
 
+// Return all uploads IDs with full path of each upload-id directory.
+// Do not return an error as this is a lazy operation
+func (fs *FSObjects) getAllUploadIDs(ctx context.Context) (result map[string]string) {
+	result = make(map[string]string)
+
+	entries, err := readDir(pathJoin(fs.fsPath, minioMetaMultipartBucket))
+	if err != nil {
+		return
+	}
+	for _, entry := range entries {
+		uploadIDs, err := readDir(pathJoin(fs.fsPath, minioMetaMultipartBucket, entry))
+		if err != nil {
+			continue
+		}
+		// Remove the trailing slash separator
+		for i := range uploadIDs {
+			uploadID := strings.TrimSuffix(uploadIDs[i], SlashSeparator)
+			result[uploadID] = pathJoin(fs.fsPath, minioMetaMultipartBucket, entry, uploadID)
+		}
+	}
+	return
+}
+
 // Removes multipart uploads if any older than `expiry` duration
 // on all buckets for every `cleanupInterval`, this function is
 // blocking and should be run in a go-routine.
 func (fs *FSObjects) cleanupStaleUploads(ctx context.Context) {
-	timer := time.NewTimer(globalAPIConfig.getStaleUploadsCleanupInterval())
-	defer timer.Stop()
+	expiryUploadsTimer := time.NewTimer(globalAPIConfig.getStaleUploadsCleanupInterval())
+	defer expiryUploadsTimer.Stop()
+
+	bgAppendTmpCleaner := time.NewTimer(bgAppendsCleanupInterval)
+	defer bgAppendTmpCleaner.Stop()
 
 	for {
 		select {
 		case <-ctx.Done():
 			return
-		case <-timer.C:
-			// Reset for the next interval
-			timer.Reset(globalAPIConfig.getStaleUploadsCleanupInterval())
+		case <-bgAppendTmpCleaner.C:
+			bgAppendTmpCleaner.Reset(bgAppendsCleanupInterval)
 
-			expiry := globalAPIConfig.getStaleUploadsExpiry()
+			foundUploadIDs := fs.getAllUploadIDs(ctx)
 
-			now := time.Now()
-			entries, err := readDir(pathJoin(fs.fsPath, minioMetaMultipartBucket))
+			// Remove background append map from the memory
+			fs.appendFileMapMu.Lock()
+			for uploadID := range fs.appendFileMap {
+				_, ok := foundUploadIDs[uploadID]
+				if !ok {
+					delete(fs.appendFileMap, uploadID)
+				}
+			}
+			fs.appendFileMapMu.Unlock()
+
+			// Remove background appends file from the disk
+			bgAppendsDir := pathJoin(fs.fsPath, minioMetaTmpBucket, fs.fsUUID, bgAppendsDirName)
+			entries, err := readDir(bgAppendsDir)
 			if err != nil {
-				continue
+				break
 			}
 			for _, entry := range entries {
-				uploadIDs, err := readDir(pathJoin(fs.fsPath, minioMetaMultipartBucket, entry))
+				uploadID := strings.Split(entry, ".")[0]
+				_, ok := foundUploadIDs[uploadID]
+				if !ok {
+					fsRemoveFile(ctx, pathJoin(bgAppendsDir, entry))
+				}
+			}
+
+		case <-expiryUploadsTimer.C:
+			// Reset for the next interval
+			expiryUploadsTimer.Reset(globalAPIConfig.getStaleUploadsCleanupInterval())
+
+			expiry := globalAPIConfig.getStaleUploadsExpiry()
+			now := time.Now()
+
+			uploadIDs := fs.getAllUploadIDs(ctx)
+
+			for uploadID, path := range uploadIDs {
+				fi, err := fsStatDir(ctx, path)
 				if err != nil {
 					continue
 				}
+				if now.Sub(fi.ModTime()) > expiry {
+					fsRemoveAll(ctx, path)
+					// Remove upload ID parent directory if empty
+					fsRemoveDir(ctx, filepath.Base(path))
 
-				// Remove the trailing slash separator
-				for i := range uploadIDs {
-					uploadIDs[i] = strings.TrimSuffix(uploadIDs[i], SlashSeparator)
-				}
-
-				for _, uploadID := range uploadIDs {
-					fi, err := fsStatDir(ctx, pathJoin(fs.fsPath, minioMetaMultipartBucket, entry, uploadID))
-					if err != nil {
-						continue
-					}
-					if now.Sub(fi.ModTime()) > expiry {
-						fsRemoveAll(ctx, pathJoin(fs.fsPath, minioMetaMultipartBucket, entry, uploadID))
-						// It is safe to ignore any directory not empty error (in case there were multiple uploadIDs on the same object)
-						fsRemoveDir(ctx, pathJoin(fs.fsPath, minioMetaMultipartBucket, entry))
-
-						// Remove uploadID from the append file map and its corresponding temporary file
-						fs.appendFileMapMu.Lock()
-						bgAppend, ok := fs.appendFileMap[uploadID]
-						if ok {
-							_ = fsRemoveFile(ctx, bgAppend.filePath)
-							delete(fs.appendFileMap, uploadID)
-						}
-						fs.appendFileMapMu.Unlock()
+					// Remove uploadID from the append file map and its corresponding temporary file
+					fs.appendFileMapMu.Lock()
+					bgAppend, ok := fs.appendFileMap[uploadID]
+					if ok {
+						_ = fsRemoveFile(ctx, bgAppend.filePath)
+						delete(fs.appendFileMap, uploadID)
 					}
+					fs.appendFileMapMu.Unlock()
 				}
 			}
 		}
diff --git a/cmd/fs-v1.go b/cmd/fs-v1.go
index c26fa8e25..c5b7a634c 100644
--- a/cmd/fs-v1.go
+++ b/cmd/fs-v1.go
@@ -106,6 +106,10 @@ func initMetaVolumeFS(fsPath, fsUUID string) error {
 		return err
 	}
 
+	if err := os.MkdirAll(pathJoin(metaTmpPath, bgAppendsDirName), 0o777); err != nil {
+		return err
+	}
+
 	if err := os.MkdirAll(pathJoin(fsPath, dataUsageBucket), 0o777); err != nil {
 		return err
 	}