diff --git a/scaladoc/src/dotty/tools/scaladoc/ScaladocSettings.scala b/scaladoc/src/dotty/tools/scaladoc/ScaladocSettings.scala
index c9561d7eb56d..390bc653f246 100644
--- a/scaladoc/src/dotty/tools/scaladoc/ScaladocSettings.scala
+++ b/scaladoc/src/dotty/tools/scaladoc/ScaladocSettings.scala
@@ -121,7 +121,7 @@ class ScaladocSettings extends SettingGroup with AllScalaSettings:
     BooleanSetting("-Ygenerate-inkuire", "Generates InkuireDB and enables Hoogle-like searches", false)
 
   val apiSubdirectory: Setting[Boolean] =
-    BooleanSetting("-Yapi-subdirectory", "Keep all api member inside `api` directory", false)
+    BooleanSetting("-Yapi-subdirectory", "Put the API documentation pages inside a directory `api/`", false)
 
   def scaladocSpecificSettings: Set[Setting[_]] =
     Set(sourceLinks, syntax, revision, externalDocumentationMappings, socialLinks, skipById, skipByRegex, deprecatedSkipPackages, docRootContent, snippetCompiler, snippetCompilerDebug, generateInkuire)
diff --git a/scaladoc/src/dotty/tools/scaladoc/renderers/HtmlRenderer.scala b/scaladoc/src/dotty/tools/scaladoc/renderers/HtmlRenderer.scala
index c35f98c24a6d..bd468273d6c7 100644
--- a/scaladoc/src/dotty/tools/scaladoc/renderers/HtmlRenderer.scala
+++ b/scaladoc/src/dotty/tools/scaladoc/renderers/HtmlRenderer.scala
@@ -64,13 +64,14 @@ class HtmlRenderer(rootPackage: Member, val members: Map[DRI, Member])(using ctx
           children = Nil
         ))
       case Some(siteContext) =>
-        // In case that we do not have an index page and we do not have any API entries 
+        // In case that we do not have an index page and we do not have any API entries
         // we want to create empty index page, so there is one
-        val actualIndexTemplate = siteContext.indexTemplates() match
-          case Nil if effectiveMembers.isEmpty => Seq(siteContext.emptyIndexTemplate)
-          case templates => templates
+        val actualIndexTemplate = siteContext.indexTemplate() match {
+            case None if effectiveMembers.isEmpty => Seq(siteContext.emptyIndexTemplate)
+            case templates => templates.toSeq
+          }
 
-        (siteContext.orphanedTemplates ++ actualIndexTemplate).map(templateToPage(_, siteContext))
+          (siteContext.orphanedTemplates ++ actualIndexTemplate).map(templateToPage(_, siteContext))
 
   /**
    * Here we have to retrive index pages from hidden pages and replace fake index pages in navigable page tree.
diff --git a/scaladoc/src/dotty/tools/scaladoc/site/StaticSiteContext.scala b/scaladoc/src/dotty/tools/scaladoc/site/StaticSiteContext.scala
index 8bf88cf47fee..b2175a9c58ec 100644
--- a/scaladoc/src/dotty/tools/scaladoc/site/StaticSiteContext.scala
+++ b/scaladoc/src/dotty/tools/scaladoc/site/StaticSiteContext.scala
@@ -25,7 +25,8 @@ class StaticSiteContext(
     if files.size > 1 then
       val msg = s"ERROR: Multiple root index pages found: ${files.map(_.getAbsolutePath)}"
       report.error(msg)
-    files
+
+    files.headOption
 
   def hasIndexFile = indexFiles.nonEmpty
 
@@ -33,7 +34,8 @@ class StaticSiteContext(
     val fakeFile = new File(root, "index.html")
     LoadedTemplate(emptyTemplate(fakeFile, "index"), List.empty, fakeFile)
 
-  def indexTemplates(): Seq[LoadedTemplate] = indexFiles.flatMap(loadTemplate(_, isBlog = false))
+  def indexTemplate(): Option[LoadedTemplate] =
+    indexFiles.flatMap(loadTemplate(_, isBlog = false))
 
   lazy val layouts: Map[String, TemplateFile] =
     val layoutRoot = new File(root, "_layouts")