diff --git a/main/src/main/scala/sbt/internal/Act.scala b/main/src/main/scala/sbt/internal/Act.scala
index a3662ac44..21d1e6c9c 100644
--- a/main/src/main/scala/sbt/internal/Act.scala
+++ b/main/src/main/scala/sbt/internal/Act.scala
@@ -63,7 +63,7 @@ object Act {
       keyMap: Map[String, AttributeKey[?]],
       data: Def.Settings
   ): Parser[ScopedKey[Any]] =
-    scopedKeySelected(index, current, defaultConfigs, keyMap, data, askProject = true)
+    scopedKeySelected(index, current, defaultConfigs, keyMap, data, askProject = true, None)
       .map(_.key.asInstanceOf[ScopedKey[Any]])
 
   // the index should be an aggregated index for proper tab completion
@@ -80,6 +80,7 @@ object Act {
           structure.index.keyMap,
           structure.data,
           askProject = true,
+          structure = Some(structure),
         )
       )
       yield Aggregation.aggregate(
@@ -102,6 +103,7 @@ object Act {
         structure.index.keyMap,
         structure.data,
         askProject = optQuery.isEmpty,
+        structure = Some(structure),
       )
     yield Aggregation
       .aggregate(selected.key, selected.mask, structure.extra)
@@ -117,10 +119,11 @@ object Act {
       keyMap: Map[String, AttributeKey[?]],
       data: Def.Settings,
       askProject: Boolean,
+      structure: Option[BuildStructure],
   ): Parser[ParsedKey] =
     scopedKeyFull(index, current, defaultConfigs, keyMap, askProject = askProject).flatMap {
       choices =>
-        select(choices, data)(using showRelativeKey2(current))
+        select(choices, data, structure)(using showRelativeKey2(current))
     }
 
   def scopedKeyFull(
@@ -197,16 +200,39 @@ object Act {
       key
     )
 
-  def select(allKeys: Seq[Parser[ParsedKey]], data: Def.Settings)(using
-      show: Show[ScopedKey[?]]
-  ): Parser[ParsedKey] =
+  def select(
+      allKeys: Seq[Parser[ParsedKey]],
+      data: Def.Settings
+  )(using show: Show[ScopedKey[?]]): Parser[ParsedKey] =
+    select(allKeys, data, None)
+
+  def select(
+      allKeys: Seq[Parser[ParsedKey]],
+      data: Def.Settings,
+      structure: Option[BuildStructure]
+  )(using show: Show[ScopedKey[?]]): Parser[ParsedKey] =
     seq(allKeys) flatMap { ss =>
       val default: Parser[ParsedKey] = ss.headOption match
         case None    => noValidKeys
         case Some(x) => success(x)
-      selectFromValid(ss filter isValid(data), default)
+      val validFilter = structure.fold(isValid(data))(isValidForAggregate(data, _))
+      selectFromValid(ss filter validFilter, default)
     }
 
+  private def isValidForAggregate(
+      data: Def.Settings,
+      structure: BuildStructure
+  )(parsed: ParsedKey): Boolean =
+    if data.contains(parsed.key) then true
+    else
+      val aggregated =
+        Aggregation.aggregate(
+          parsed.key.asInstanceOf[ScopedKey[Any]],
+          parsed.mask,
+          structure.extra
+        )
+      aggregated.nonEmpty && aggregated.exists(data.contains)
+
   def selectFromValid(ss: Seq[ParsedKey], default: Parser[ParsedKey])(using
       show: Show[ScopedKey[?]]
   ): Parser[ParsedKey] =
@@ -230,7 +256,7 @@ object Act {
     if (zeros.nonEmpty) zeros else selects
   }
 
-  def noValidKeys = failure("No such key.")
+  def noValidKeys: Parser[ParsedKey] = failure("No such key.")
 
   def showAmbiguous(keys: Seq[ScopedKey[?]])(using show: Show[ScopedKey[?]]): String =
     keys.take(3).map(x => show.show(x)).mkString("", ", ", if (keys.size > 3) ", ..." else "")
diff --git a/main/src/main/scala/sbt/internal/Load.scala b/main/src/main/scala/sbt/internal/Load.scala
index 2d016305d..83623cf3b 100755
--- a/main/src/main/scala/sbt/internal/Load.scala
+++ b/main/src/main/scala/sbt/internal/Load.scala
@@ -867,7 +867,7 @@ private[sbt] object Load {
             defaultProjects.generatedConfigClassFiles ++ loadedProjectsRaw.generatedConfigClassFiles
           )
         }
-      val loadedProjects = processAutoAggregate(loadedProjects0, uri)
+      val loadedProjects = processAutoAggregate(loadedProjects0, uri, normBase, !hasRoot)
       timed("Load.loadUnit: cleanEvalClasses", log) {
         cleanEvalClasses(defDir, keepClassFiles)
       }
@@ -889,9 +889,29 @@ private[sbt] object Load {
       new BuildUnit(uri, normBase, loadedDefs, plugs, converter)
     }
 
-  private def processAutoAggregate(inProjects: Seq[Project], uri: URI): Seq[Project] =
-    inProjects.map: proj =>
-      proj
+  private def processAutoAggregate(
+      inProjects: Seq[Project],
+      uri: URI,
+      buildBase: File,
+      hasAutoRoot: Boolean
+  ): Seq[Project] =
+    if !hasAutoRoot then inProjects
+    else
+      val allProjectIds = inProjects.map(_.id).toSet
+      inProjects.map: proj =>
+        val isAutoRoot = isRootPath(proj.base, buildBase) && proj.aggregate.nonEmpty
+        if isAutoRoot then
+          val currentAggregateIds = proj.aggregate
+            .flatMap:
+              case ref: ProjectRef => Some(ref.project)
+              case _               => None
+            .toSet
+          val missingIds = allProjectIds - proj.id -- currentAggregateIds
+          if missingIds.nonEmpty then
+            val missingRefs = missingIds.toSeq.map(id => ProjectRef(uri, id))
+            proj.aggregate((proj.aggregate ++ missingRefs)*)
+          else proj
+        else proj
 
   private def autoID(
       localBase: File,
diff --git a/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/build.sbt b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/build.sbt
new file mode 100644
index 000000000..415a43679
--- /dev/null
+++ b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/build.sbt
@@ -0,0 +1,16 @@
+/*
+ * sbt
+ * Copyright 2023, Scala center
+ * Copyright 2011 - 2022, Lightbend, Inc.
+ * Copyright 2008 - 2010, Mark Harrah
+ * Licensed under Apache License 2.0 (see LICENSE)
+ */
+
+val check = taskKey[Unit]("Repro for #4947: task at root when extraProjects creates auto root")
+
+val a = project
+val p = project
+  .settings(
+    name := "p",
+    check := ()
+  )
diff --git a/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/project/ExtraPlugin.scala b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/project/ExtraPlugin.scala
new file mode 100644
index 000000000..77ff44de2
--- /dev/null
+++ b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/project/ExtraPlugin.scala
@@ -0,0 +1,15 @@
+/*
+ * sbt
+ * Copyright 2023, Scala center
+ * Copyright 2011 - 2022, Lightbend, Inc.
+ * Copyright 2008 - 2010, Mark Harrah
+ * Licensed under Apache License 2.0 (see LICENSE)
+ */
+
+import sbt._, Keys._
+
+object ExtraPlugin extends AutoPlugin {
+  override def trigger = allRequirements
+  override def extraProjects: Seq[Project] =
+    Seq(Project("z", file("z")).settings(name := "z"))
+}
diff --git a/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/test b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/test
new file mode 100644
index 000000000..15675b169
--- /dev/null
+++ b/sbt-app/src/sbt-test/project/extra-projects-key-aggregate/test
@@ -0,0 +1 @@
+> check