diff --git a/main/src/main/scala/sbt/internal/Aggregation.scala b/main/src/main/scala/sbt/internal/Aggregation.scala
index 874e1d2b7..b5c3f811b 100644
--- a/main/src/main/scala/sbt/internal/Aggregation.scala
+++ b/main/src/main/scala/sbt/internal/Aggregation.scala
@@ -239,13 +239,22 @@ object Aggregation {
   private def maps[T, S](vs: Values[T])(f: T => S): Values[S] =
     vs map { case KeyValue(k, v) => KeyValue(k, f(v)) }
 
+  /**
+   * Returns the aggregated projects for the given reference.
+   * Build-level references (ThisBuild, BuildRef) do not aggregate - only project-level
+   * references participate in aggregation. This fixes issue #5349 where ThisBuild-scoped
+   * keys incorrectly used the root project's aggregates.
+   */
   def projectAggregates[Proj](
       proj: Option[Reference],
       extra: BuildUtil[Proj],
       reverse: Boolean
   ): Seq[ProjectRef] =
-    val resRef = proj.map(p => extra.projectRefFor(extra.resolveRef(p)))
-    resRef.toList.flatMap { ref =>
+    val projectRef = proj.flatMap {
+      case _: BuildReference => None
+      case ref               => Some(extra.projectRefFor(extra.resolveRef(ref)))
+    }
+    projectRef.toList.flatMap { ref =>
       if reverse then extra.aggregates.reverse(ref)
       else extra.aggregates.forward(ref)
     }
diff --git a/main/src/test/scala/sbt/internal/AggregationSpec.scala b/main/src/test/scala/sbt/internal/AggregationSpec.scala
index d2f440b9e..bb4fbed5d 100644
--- a/main/src/test/scala/sbt/internal/AggregationSpec.scala
+++ b/main/src/test/scala/sbt/internal/AggregationSpec.scala
@@ -8,9 +8,35 @@
 
 package sbt.internal
 
+import java.net.URI
+import sbt.{ BuildRef, Def, Scope }
+import sbt.Def.ScopedKey
+import sbt.ScopeAxis.{ Select, Zero }
+import sbt.internal.TestBuild.{ Build, Env, Proj, Taskk }
+import sbt.internal.util.AttributeKey
+import sbt.librarymanagement.Configuration
+
 object AggregationSpec extends verify.BasicTestSuite {
   val timing = Aggregation.timing(0, _: Long)
 
+  test(
+    "projectAggregates should return empty for BuildRef (ThisBuild-scoped keys do not aggregate, #5349)"
+  ) {
+    val buildURI = new URI("file", "///path/", null)
+    val config = Configuration.of("Compile", "compile")
+    val project = Proj("root", Nil, Seq(config))
+    val build = Build(buildURI, Vector(project))
+    val key = AttributeKey[String]("test")
+    val task = Taskk(key, Nil)
+    val env = Env(Vector(build), Vector(task))
+    val scope = Scope(Select(BuildRef(buildURI)), Zero, Select(key), Zero)
+    val settings = Seq(Def.setting(ScopedKey(scope, key), Def.value("v")))
+    val structure = TestBuild.structure(env, settings, build.allProjects.head._1)
+    val result =
+      Aggregation.projectAggregates(Some(BuildRef(buildURI)), structure.extra, reverse = false)
+    assert(result.isEmpty, s"BuildRef must not aggregate; got: $result")
+  }
+
   test("timing should format total time properly") {
     assert(timing(101).startsWith("elapsed time: 0 s"))
     assert(timing(1000).startsWith("elapsed time: 1 s"))
diff --git a/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/build.sbt b/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/build.sbt
new file mode 100644
index 000000000..17abf53aa
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/build.sbt
@@ -0,0 +1,31 @@
+ThisBuild / scalaVersion := "2.13.16"
+
+lazy val mark = taskKey[Unit]("Creates a marker file to track where this task ran")
+
+lazy val root = (project in file("."))
+  .aggregate(sub)
+  .settings(
+    name := "root",
+    mark := {
+      val toMark = baseDirectory.value / "root-ran"
+      if (toMark.exists) sys.error(s"Already ran ($toMark exists)")
+      else IO.touch(toMark)
+    }
+  )
+
+lazy val sub = (project in file("sub"))
+  .settings(
+    name := "sub",
+    mark := {
+      val toMark = baseDirectory.value / "sub-ran"
+      if (toMark.exists) sys.error(s"Already ran ($toMark exists)")
+      else IO.touch(toMark)
+    }
+  )
+
+ThisBuild / mark := {
+  val base = (ThisBuild / baseDirectory).value
+  val toMark = base / "build-ran"
+  if (toMark.exists) sys.error(s"Already ran ($toMark exists)")
+  else IO.touch(toMark)
+}
diff --git a/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/test b/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/test
new file mode 100644
index 000000000..7a32a7989
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/thisbuild-no-aggregate/test
@@ -0,0 +1,19 @@
+# Verify ThisBuild-scoped keys do not participate in aggregation (sbt/sbt#5349, PR #8703).
+# Each scope level has its own mark task creating distinct files:
+#   - ThisBuild/mark creates build-ran
+#   - root/mark creates root-ran
+#   - sub/mark creates sub-ran
+# Before the fix, "show ThisBuild/mark" would aggregate and run root+sub marks.
+# After the fix, it runs only the build-level task.
+$ mkdir sub
+
+# ThisBuild/mark should only create build-ran, not trigger root or sub
+> show ThisBuild/mark
+$ exists build-ran
+$ absent root-ran
+$ absent sub/sub-ran
+
+# Verify project-level marks still work and do aggregate
+> show root/mark
+$ exists root-ran
+$ exists sub/sub-ran