diff --git a/pkg/storage/engine_test.go b/pkg/storage/engine_test.go
index c656e3172b8d..ca2d51e8c5cb 100644
--- a/pkg/storage/engine_test.go
+++ b/pkg/storage/engine_test.go
@@ -34,10 +34,12 @@ import (
 	"github.com/cockroachdb/cockroach/pkg/storage/enginepb"
 	"github.com/cockroachdb/cockroach/pkg/storage/fs"
 	"github.com/cockroachdb/cockroach/pkg/testutils"
+	"github.com/cockroachdb/cockroach/pkg/testutils/skip"
 	"github.com/cockroachdb/cockroach/pkg/util/hlc"
 	"github.com/cockroachdb/cockroach/pkg/util/leaktest"
 	"github.com/cockroachdb/cockroach/pkg/util/log"
 	"github.com/cockroachdb/cockroach/pkg/util/protoutil"
+	"github.com/cockroachdb/cockroach/pkg/util/randutil"
 	"github.com/cockroachdb/cockroach/pkg/util/uuid"
 	"github.com/cockroachdb/errors"
 	"github.com/cockroachdb/errors/oserror"
@@ -1031,6 +1033,110 @@ func TestCreateCheckpoint(t *testing.T) {
 	}
 }
 
+func TestCreateCheckpoint_SpanConstrained(t *testing.T) {
+	defer leaktest.AfterTest(t)()
+	defer log.Scope(t).Close(t)
+	skip.WithIssue(t, 100935)
+	ctx := context.Background()
+
+	rng, _ := randutil.NewTestRand()
+	dir, cleanup := testutils.TempDir(t)
+	defer cleanup()
+
+	key := func(i int) roachpb.Key {
+		return keys.SystemSQLCodec.TablePrefix(uint32(i))
+	}
+
+	db, err := Open(
+		ctx,
+		Filesystem(dir),
+		cluster.MakeTestingClusterSettings(),
+		TargetFileSize(10<<10 /* 10 KB */),
+	)
+	assert.NoError(t, err)
+	defer db.Close()
+
+	// Write keys /Table/1/../Table/10000.
+	b := db.NewWriteBatch()
+	const maxTableID = 10000
+	for i := 1; i <= maxTableID; i++ {
+		require.NoError(t, b.PutMVCC(
+			MVCCKey{Key: key(i), Timestamp: hlc.Timestamp{WallTime: int64(i)}},
+			MVCCValue{Value: roachpb.Value{RawBytes: randutil.RandBytes(rng, 500)}},
+		))
+	}
+	require.NoError(t, b.Commit(true /* sync */))
+	require.NoError(t, db.Flush())
+
+	sstables, err := db.db.SSTables()
+	require.NoError(t, err)
+	for _, tbls := range sstables {
+		for _, tbl := range tbls {
+			t.Logf("%s: %s-%s", tbl.FileNum, tbl.Smallest, tbl.Largest)
+		}
+	}
+
+	checkpointRootDir := filepath.Join(dir, "checkpoint")
+	require.NoError(t, db.FS.MkdirAll(checkpointRootDir, os.ModePerm))
+
+	var checkpointNum int
+	checkpointSpan := func(s roachpb.Span) string {
+		checkpointNum++
+		dir := filepath.Join(checkpointRootDir, fmt.Sprintf("%06d", checkpointNum))
+		t.Logf("Writing checkpoint for span %s to %q", s, dir)
+		assert.NoError(t, db.CreateCheckpoint(dir, []roachpb.Span{s}))
+		assert.DirExists(t, dir)
+		m, err := filepath.Glob(dir + "/*")
+		assert.NoError(t, err)
+		assert.True(t, len(m) > 0)
+		t.Logf("Checkpoint wrote files: %s", strings.Join(m, ", "))
+		return dir
+	}
+	verifyCheckpoint := func(dir string, low, high int) {
+		t.Logf("Verifying checkpoint for span [%d,%d) in %q", low, high, dir)
+		// Verify that we can open the checkpoint.
+		cDB, err := Open(
+			ctx,
+			Filesystem(dir),
+			cluster.MakeTestingClusterSettings(),
+			MustExist)
+		require.NoError(t, err)
+		defer cDB.Close()
+
+		iter := cDB.NewMVCCIterator(MVCCKeyIterKind, IterOptions{
+			LowerBound: key(low),
+			UpperBound: key(high),
+		})
+		defer iter.Close()
+		iter.SeekGE(MVCCKey{Key: key(low)})
+		count := 0
+		for {
+			if valid, err := iter.Valid(); !valid {
+				require.NoError(t, err)
+				break
+			}
+			count++
+			iter.Next()
+		}
+		require.Equal(t, count, high-low)
+	}
+
+	for i := 0; i < 10; i++ {
+		start := randutil.RandIntInRange(rng, 1, maxTableID)
+		end := randutil.RandIntInRange(rng, 1, maxTableID)
+		for start == end {
+			end = randutil.RandIntInRange(rng, 1, maxTableID)
+		}
+		if start > end {
+			start, end = end, start
+		}
+
+		span := roachpb.Span{Key: key(start), EndKey: key(end)}
+		dir := checkpointSpan(span)
+		verifyCheckpoint(dir, start, end)
+	}
+}
+
 func TestIngestDelayLimit(t *testing.T) {
 	defer leaktest.AfterTest(t)()
 	defer log.Scope(t).Close(t)
diff --git a/pkg/storage/open.go b/pkg/storage/open.go
index 4c5f4cbb9d08..c59e4ea9cdfb 100644
--- a/pkg/storage/open.go
+++ b/pkg/storage/open.go
@@ -107,6 +107,17 @@ func BlockSize(size int) ConfigOption {
 	}
 }
 
+// TargetFileSize sets the target file size across all levels of the LSM,
+// primarily for testing purposes.
+func TargetFileSize(size int64) ConfigOption {
+	return func(cfg *engineConfig) error {
+		for i := range cfg.Opts.Levels {
+			cfg.Opts.Levels[i].TargetFileSize = size
+		}
+		return nil
+	}
+}
+
 // MaxWriterConcurrency sets the concurrency of the sstable Writers. A concurrency
 // of 0 implies no parallelism in the Writer, and a concurrency of 1 or more implies
 // parallelism in the Writer. Currently, there's no difference between a concurrency
diff --git a/pkg/storage/pebble.go b/pkg/storage/pebble.go
index 7f546f39fb1b..dafb70cbce8b 100644
--- a/pkg/storage/pebble.go
+++ b/pkg/storage/pebble.go
@@ -1950,7 +1950,10 @@ func (p *Pebble) CreateCheckpoint(dir string, spans []roachpb.Span) error {
 	if l := len(spans); l > 0 {
 		s := make([]pebble.CheckpointSpan, 0, l)
 		for _, span := range spans {
-			s = append(s, pebble.CheckpointSpan{Start: span.Key, End: span.EndKey})
+			s = append(s, pebble.CheckpointSpan{
+				Start: EngineKey{Key: span.Key}.Encode(),
+				End:   EngineKey{Key: span.EndKey}.Encode(),
+			})
 		}
 		opts = append(opts, pebble.WithRestrictToSpans(s))
 	}