diff --git a/pkg/compactor/compactor.go b/pkg/compactor/compactor.go
index fe1ad01d028..58a9360b304 100644
--- a/pkg/compactor/compactor.go
+++ b/pkg/compactor/compactor.go
@@ -7,7 +7,6 @@ import (
 	"hash/fnv"
 	"math/rand"
 	"os"
-	"path"
 	"path/filepath"
 	"strings"
 	"time"
@@ -832,7 +831,7 @@ func (c *Compactor) compactUser(ctx context.Context, userID string) error {
 		c.blocksGrouperFactory(currentCtx, c.compactorCfg, bucket, ulogger, reg, c.blocksMarkedForDeletion, c.blocksMarkedForNoCompaction, c.garbageCollectedBlocks, c.remainingPlannedCompactions, c.blockVisitMarkerReadFailed, c.blockVisitMarkerWriteFailed, c.ring, c.ringLifecycler, c.limits, userID, noCompactMarkerFilter),
 		c.blocksPlannerFactory(currentCtx, bucket, ulogger, c.compactorCfg, noCompactMarkerFilter, c.ringLifecycler, c.blockVisitMarkerReadFailed, c.blockVisitMarkerWriteFailed),
 		c.blocksCompactor,
-		path.Join(c.compactorCfg.DataDir, "compact"),
+		c.compactDirForUser(userID),
 		bucket,
 		c.compactorCfg.CompactionConcurrency,
 		c.compactorCfg.SkipBlocksWithOutOfOrderChunksEnabled,
@@ -845,6 +844,13 @@ func (c *Compactor) compactUser(ctx context.Context, userID string) error {
 		return errors.Wrap(err, "compaction")
 	}
 
+	// Remove all files on the compact root dir
+	// We do this only if there is no error because potentially on the next run we would not have to download
+	// everything again.
+	if err := os.RemoveAll(c.compactRootDir()); err != nil {
+		level.Error(c.logger).Log("msg", "failed to remove compaction work directory", "path", c.compactRootDir(), "err", err)
+	}
+
 	return nil
 }
 
@@ -941,6 +947,16 @@ func (c *Compactor) metaSyncDirForUser(userID string) string {
 	return filepath.Join(c.compactorCfg.DataDir, compactorMetaPrefix+userID)
 }
 
+// compactDirForUser returns the directory to be used to download and compact the blocks for a user
+func (c *Compactor) compactDirForUser(userID string) string {
+	return filepath.Join(c.compactRootDir(), userID)
+}
+
+// compactRootDir returns the root directory to be used to download and compact blocks
+func (c *Compactor) compactRootDir() string {
+	return filepath.Join(c.compactorCfg.DataDir, "compact")
+}
+
 // This function returns tenants with meta sync directories found on local disk. On error, it returns nil map.
 func (c *Compactor) listTenantsWithMetaSyncDirectories() map[string]struct{} {
 	result := map[string]struct{}{}
diff --git a/pkg/compactor/compactor_test.go b/pkg/compactor/compactor_test.go
index 99c5753e064..3e880418f4f 100644
--- a/pkg/compactor/compactor_test.go
+++ b/pkg/compactor/compactor_test.go
@@ -539,6 +539,47 @@ func TestCompactor_ShouldIncrementCompactionErrorIfFailedToCompactASingleTenant(
 	))
 }
 
+func TestCompactor_ShouldCompactAndRemoveUserFolder(t *testing.T) {
+	bucketClient := &bucket.ClientMock{}
+	bucketClient.MockIter("", []string{"user-1"}, nil)
+	bucketClient.MockExists(path.Join("user-1", cortex_tsdb.TenantDeletionMarkPath), false, nil)
+	bucketClient.MockIter("user-1/", []string{"user-1/01DTVP434PA9VFXSW2JKB3392D/meta.json", "user-1/01FN6CDF3PNEWWRY5MPGJPE3EX/meta.json"}, nil)
+	bucketClient.MockIter("user-1/markers/", nil, nil)
+	bucketClient.MockGet("user-1/01DTVP434PA9VFXSW2JKB3392D/meta.json", mockBlockMetaJSON("01DTVP434PA9VFXSW2JKB3392D"), nil)
+	bucketClient.MockGet("user-1/01DTVP434PA9VFXSW2JKB3392D/deletion-mark.json", "", nil)
+	bucketClient.MockGet("user-1/01DTVP434PA9VFXSW2JKB3392D/no-compact-mark.json", "", nil)
+	bucketClient.MockGet("user-1/01DTVP434PA9VFXSW2JKB3392D/visit-mark.json", "", nil)
+	bucketClient.MockGet("user-1/bucket-index-sync-status.json", "", nil)
+	bucketClient.MockGet("user-1/01FN6CDF3PNEWWRY5MPGJPE3EX/meta.json", mockBlockMetaJSON("01FN6CDF3PNEWWRY5MPGJPE3EX"), nil)
+	bucketClient.MockGet("user-1/01FN6CDF3PNEWWRY5MPGJPE3EX/deletion-mark.json", "", nil)
+	bucketClient.MockGet("user-1/01FN6CDF3PNEWWRY5MPGJPE3EX/no-compact-mark.json", "", nil)
+	bucketClient.MockGet("user-1/01FN6CDF3PNEWWRY5MPGJPE3EX/visit-mark.json", "", nil)
+	bucketClient.MockGet("user-1/bucket-index.json.gz", "", nil)
+	bucketClient.MockGet("user-1/bucket-index-sync-status.json", "", nil)
+	bucketClient.MockIter("user-1/markers/", nil, nil)
+	bucketClient.MockUpload("user-1/bucket-index.json.gz", nil)
+	bucketClient.MockUpload("user-1/bucket-index-sync-status.json", nil)
+
+	c, _, tsdbPlanner, _, _ := prepare(t, prepareConfig(), bucketClient, nil)
+
+	// Make sure the user folder is created and is being used
+	// This will be called during compaction
+	tsdbPlanner.On("Plan", mock.Anything, mock.Anything, mock.Anything, mock.Anything).Run(func(args mock.Arguments) {
+		_, err := os.Stat(c.compactDirForUser("user-1"))
+		require.NoError(t, err)
+	}).Return([]*metadata.Meta{}, nil)
+
+	require.NoError(t, services.StartAndAwaitRunning(context.Background(), c))
+
+	// Wait until a run has completed.
+	cortex_testutil.Poll(t, time.Second, 1.0, func() interface{} {
+		return prom_testutil.ToFloat64(c.compactionRunsCompleted)
+	})
+
+	_, err := os.Stat(c.compactDirForUser("user-1"))
+	require.True(t, os.IsNotExist(err))
+}
+
 func TestCompactor_ShouldIterateOverUsersAndRunCompaction(t *testing.T) {
 	t.Parallel()