diff --git a/main-actions/src/main/scala/sbt/Tests.scala b/main-actions/src/main/scala/sbt/Tests.scala
index 61dda1875..c5b7c82d7 100644
--- a/main-actions/src/main/scala/sbt/Tests.scala
+++ b/main-actions/src/main/scala/sbt/Tests.scala
@@ -281,8 +281,23 @@ object Tests {
       if (orderedFilters.isEmpty) filtered0
       else orderedFilters.flatMap(f => filtered0.filter(d => f(d.name))).toList.distinct
     val uniqueTests = distinctBy(tests)(_.name)
+    // When user ran testOnly with explicit args and the filter restricted the set, mark matching
+    // tests as explicitlySpecified so frameworks (e.g. ScalaTest) can run @DoNotDiscover suites.
+    // Do not mark when orderedFilters is "run all" (e.g. test with no args -> selectedFilter(Nil) -> match all).
+    val filteredToSubset = orderedFilters.nonEmpty && uniqueTests.size < discovered.size
+    val testsToUse =
+      if (!filteredToSubset) uniqueTests
+      else
+        uniqueTests.map(t =>
+          new TestDefinition(
+            t.name,
+            t.fingerprint,
+            explicitlySpecified = true,
+            Array(new SuiteSelector: Selector)
+          )
+        )
     new ProcessedOptions(
-      uniqueTests.toVector,
+      testsToUse.toVector,
       setup.toVector,
       cleanup.toVector,
       testListeners.toVector
@@ -555,7 +570,6 @@ object Tests {
         c.topLevel
       case _ => false
     })
-    // TODO: To pass in correct explicitlySpecified and selectors
     val tests =
       for {
         (df, di) <- discovered
diff --git a/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/build.sbt b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/build.sbt
new file mode 100644
index 000000000..8cd9690fa
--- /dev/null
+++ b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/build.sbt
@@ -0,0 +1,9 @@
+val scalatest = "org.scalatest" %% "scalatest" % "3.0.5"
+
+ThisBuild / scalaVersion := "2.12.21"
+
+lazy val root = (project in file("."))
+  .settings(
+    libraryDependencies += scalatest,
+    Test / testOptions += Tests.Argument("-C", "custom.CustomReporter")
+  )
diff --git a/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/main/scala/custom/CustomReporter.scala b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/main/scala/custom/CustomReporter.scala
new file mode 100644
index 000000000..d3f20a21b
--- /dev/null
+++ b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/main/scala/custom/CustomReporter.scala
@@ -0,0 +1,30 @@
+package custom
+
+import java.io._
+import org.scalatest._
+import events._
+
+class CustomReporter extends Reporter {
+
+	private def writeFile(filePath: String, content: String): Unit = {
+		val file = new File(filePath)
+		val writer =
+			if (!file.exists)
+				new FileWriter(new File(filePath))
+			else
+				new FileWriter(new File(filePath + "-2"))
+		writer.write(content)
+		writer.flush()
+		writer.close()
+	}
+
+	def apply(event: Event): Unit = {
+		event match {
+			case SuiteStarting(_, suiteName, _, _, _, _, _, _, _, _) => writeFile("target/SuiteStarting-" + suiteName, suiteName)
+			case SuiteCompleted(_, suiteName, _, _, _, _, _, _, _, _, _) => writeFile("target/SuiteCompleted-" + suiteName, suiteName)
+			case TestStarting(_, _, _, _, testName, _, _, _, _, _, _, _) => writeFile("target/TestStarting-" + testName, testName)
+			case TestSucceeded(_, _, _, _, testName, _, _, _, _, _, _, _, _, _) => writeFile("target/TestSucceeded-" + testName, testName)
+			case _ =>
+		}
+	}
+}
diff --git a/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec.scala b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec.scala
new file mode 100644
index 000000000..05c155b63
--- /dev/null
+++ b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec.scala
@@ -0,0 +1,12 @@
+package com.test
+
+import org.scalatest.Spec
+
+class TestSpec extends Spec {
+
+	def `TestSpec-test-1 ` {}
+
+	def `TestSpec-test-2 ` {}
+	
+	def `TestSpec-test-3 ` {}
+}
diff --git a/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec2.scala b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec2.scala
new file mode 100644
index 000000000..1ff28dffc
--- /dev/null
+++ b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/src/test/scala/com/test/TestSpec2.scala
@@ -0,0 +1,13 @@
+package com.test
+
+import org.scalatest._
+
+@DoNotDiscover
+class TestSpec2 extends Spec {
+
+	def `TestSpec2-test-1 ` {}
+
+	def `TestSpec2-test-2 ` {}
+	
+	def `TestSpec2-test-3 ` {}
+}
diff --git a/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/test b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/test
new file mode 100644
index 000000000..2391b2260
--- /dev/null
+++ b/sbt-app/src/sbt-test/tests/i5609-do-not-discover-testonly/test
@@ -0,0 +1,5 @@
+# #5609: When explicitly requested via testOnly, @DoNotDiscover suite should run
+> clean
+> testOnly com.test.TestSpec2
+$ exists target/SuiteStarting-TestSpec2
+$ exists target/SuiteCompleted-TestSpec2