diff --git a/pruner/light/pruner.go b/pruner/light/pruner.go
index 296e100fc1..8986f81d10 100644
--- a/pruner/light/pruner.go
+++ b/pruner/light/pruner.go
@@ -4,20 +4,28 @@ import (
 	"context"
 
 	"github.com/ipfs/boxo/blockservice"
+	"github.com/ipfs/go-datastore"
 
 	"github.com/celestiaorg/celestia-node/header"
+	"github.com/celestiaorg/celestia-node/share"
 	"github.com/celestiaorg/celestia-node/share/ipld"
 )
 
 type Pruner struct {
 	bserv blockservice.BlockService
+	ds    datastore.Datastore
 }
 
-func NewPruner(bserv blockservice.BlockService) *Pruner {
-	return &Pruner{bserv: bserv}
+func NewPruner(bserv blockservice.BlockService, ds datastore.Datastore) *Pruner {
+	return &Pruner{bserv: bserv, ds: ds}
 }
 
 func (p *Pruner) Prune(ctx context.Context, h *header.ExtendedHeader) error {
+	dah := h.DAH
+	if share.DataHash(dah.Hash()).IsEmptyRoot() {
+		return nil
+	}
+
 	var roots [][]byte
 	roots = append(roots, h.DAH.RowRoots...)
 	roots = append(roots, h.DAH.ColumnRoots...)
@@ -28,5 +36,15 @@ func (p *Pruner) Prune(ctx context.Context, h *header.ExtendedHeader) error {
 		}
 	}
 
+	key := rootKey(dah)
+	err := p.ds.Delete(ctx, key)
+	if err != nil {
+		return err
+	}
+
 	return nil
 }
+
+func rootKey(root *share.Root) datastore.Key {
+	return datastore.NewKey(root.String())
+}