diff --git a/changelog/fragments/1681942680-fix-diag-zip-file.yaml b/changelog/fragments/1681942680-fix-diag-zip-file.yaml
new file mode 100644
index 00000000000..e9ee76a2563
--- /dev/null
+++ b/changelog/fragments/1681942680-fix-diag-zip-file.yaml
@@ -0,0 +1,4 @@
+kind: bug-fix
+summary: Fix diagnostic zip file handling of sub-directories in logs/.
+component: diagnostics
+pr: https://github.com/elastic/elastic-agent/pull/2523
diff --git a/internal/pkg/diagnostics/diagnostics.go b/internal/pkg/diagnostics/diagnostics.go
index f3a3965daa4..7b3df7cfdd7 100644
--- a/internal/pkg/diagnostics/diagnostics.go
+++ b/internal/pkg/diagnostics/diagnostics.go
@@ -318,6 +318,15 @@ func zipLogsWithPath(pathsHome, commitName string, collectServices bool, zw *zip
 		}
 	}
 
+	_, err = zw.CreateHeader(&zip.FileHeader{
+		Name:     "logs/" + commitName + "/",
+		Method:   zip.Deflate,
+		Modified: ts,
+	})
+	if err != nil {
+		return err
+	}
+
 	// using Data() + "/logs", for some reason default paths/Logs() is the home dir...
 	logPath := filepath.Join(pathsHome, "logs") + string(filepath.Separator)
 	return filepath.WalkDir(logPath, func(path string, d fs.DirEntry, fErr error) error {
@@ -339,7 +348,7 @@ func zipLogsWithPath(pathsHome, commitName string, collectServices bool, zw *zip
 
 		if d.IsDir() {
 			_, err := zw.CreateHeader(&zip.FileHeader{
-				Name:     "logs" + name + "/",
+				Name:     "logs/" + filepath.ToSlash(name) + "/",
 				Method:   zip.Deflate,
 				Modified: ts,
 			})
@@ -407,7 +416,7 @@ func saveLogs(name string, logPath string, zw *zip.Writer) error {
 		ts = li.ModTime()
 	}
 	zf, err := zw.CreateHeader(&zip.FileHeader{
-		Name:     "logs/" + name,
+		Name:     "logs/" + filepath.ToSlash(name),
 		Method:   zip.Deflate,
 		Modified: ts,
 	})
diff --git a/internal/pkg/diagnostics/dianostics_test.go b/internal/pkg/diagnostics/dianostics_test.go
new file mode 100644
index 00000000000..7cc2415ad82
--- /dev/null
+++ b/internal/pkg/diagnostics/dianostics_test.go
@@ -0,0 +1,57 @@
+// Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+// or more contributor license agreements. Licensed under the Elastic License;
+// you may not use this file except in compliance with the Elastic License.
+
+package diagnostics
+
+import (
+	"archive/zip"
+	"bytes"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/elastic/elastic-agent/internal/pkg/agent/application/paths"
+)
+
+func TestZipLogs(t *testing.T) {
+	// Setup a directory structure of: logs/httpjson/log.ndjson
+	{
+		paths.SetTop(t.TempDir())
+		dir := filepath.Join(paths.Home(), "logs/sub-dir")
+		require.NoError(t, os.MkdirAll(dir, 0o700))
+		require.NoError(t, os.WriteFile(filepath.Join(dir, "log.ndjson"), []byte(".\n"), 0o600))
+	}
+
+	// Zip the logs directory.
+	buf := new(bytes.Buffer)
+	w := zip.NewWriter(buf)
+	require.NoError(t, zipLogs(w, time.Now()))
+	require.NoError(t, w.Close())
+
+	type zippedItem struct {
+		Name  string
+		IsDir bool
+	}
+
+	// Read back the contents.
+	r, err := zip.NewReader(bytes.NewReader(buf.Bytes()), int64(buf.Len()))
+	require.NoError(t, err)
+	var observed []zippedItem
+	for _, f := range r.File {
+		observed = append(observed, zippedItem{Name: f.Name, IsDir: f.FileInfo().IsDir()})
+	}
+
+	// Verify the results.
+	expected := []zippedItem{
+		{"logs/", true},
+		{"logs/elastic-agent-unknow/", true},
+		{"logs/elastic-agent-unknow/sub-dir/", true},
+		{"logs/elastic-agent-unknow/sub-dir/log.ndjson", false},
+	}
+	assert.Equal(t, expected, observed)
+}