diff --git a/compiler/src/dotty/tools/dotc/sbt/ExtractAPI.scala b/compiler/src/dotty/tools/dotc/sbt/ExtractAPI.scala
index c7a05fe2f284..863909066161 100644
--- a/compiler/src/dotty/tools/dotc/sbt/ExtractAPI.scala
+++ b/compiler/src/dotty/tools/dotc/sbt/ExtractAPI.scala
@@ -604,10 +604,12 @@ private class ExtractAPICollector(using Context) extends ThunkHolder {
 
     // In the Scala2 ExtractAPI phase we only extract annotations that extend
     // StaticAnnotation, but in Dotty we currently pickle all annotations so we
-    // extract everything (except inline body annotations which are handled
-    // above).
-    s.annotations.filter(_.symbol != defn.BodyAnnot) foreach { annot =>
-      annots += apiAnnotation(annot)
+    // extract everything (except annotations missing from the classpath which
+    // we simply skip over, and inline body annotations which are handled above).
+    s.annotations.foreach { annot =>
+      val sym = annot.symbol
+      if sym.exists && sym != defn.BodyAnnot then
+        annots += apiAnnotation(annot)
     }
 
     annots.toList
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/A.scala b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/A.scala
new file mode 100644
index 000000000000..77ab340e6e4a
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/A.scala
@@ -0,0 +1,4 @@
+class A {
+  @JavaAnnot def foo: Int = 1
+  @ScalaAnnot def bar: Int = 1
+}
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/JavaAnnot.java b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/JavaAnnot.java
new file mode 100644
index 000000000000..745105f178ea
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/JavaAnnot.java
@@ -0,0 +1,3 @@
+import java.lang.annotation.*;
+
+public @interface JavaAnnot {}
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/ScalaAnnot.scala b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/ScalaAnnot.scala
new file mode 100644
index 000000000000..8b0ee32e9dbd
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/a/ScalaAnnot.scala
@@ -0,0 +1 @@
+class ScalaAnnot extends scala.annotation.StaticAnnotation
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/b/B.scala b/sbt-dotty/sbt-test/source-dependencies/missing-annot/b/B.scala
new file mode 100644
index 000000000000..a18aec3dbe9b
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/b/B.scala
@@ -0,0 +1 @@
+class B extends A
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/build.sbt b/sbt-dotty/sbt-test/source-dependencies/missing-annot/build.sbt
new file mode 100644
index 000000000000..350b46c7b27b
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/build.sbt
@@ -0,0 +1,9 @@
+lazy val a = project.in(file("a"))
+  .settings(
+    Compile / classDirectory := (ThisBuild / baseDirectory).value / "a-output"
+  )
+
+lazy val b = project.in(file("b"))
+  .settings(
+    Compile / unmanagedClasspath += (ThisBuild / baseDirectory).value / "b-input"
+  )
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/DottyInjectedPlugin.scala b/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/DottyInjectedPlugin.scala
new file mode 100644
index 000000000000..fb946c4b8c61
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/DottyInjectedPlugin.scala
@@ -0,0 +1,11 @@
+import sbt._
+import Keys._
+
+object DottyInjectedPlugin extends AutoPlugin {
+  override def requires = plugins.JvmPlugin
+  override def trigger = allRequirements
+
+  override val projectSettings = Seq(
+    scalaVersion := sys.props("plugin.scalaVersion")
+  )
+}
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/plugins.sbt b/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/plugins.sbt
new file mode 100644
index 000000000000..c17caab2d98c
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/project/plugins.sbt
@@ -0,0 +1 @@
+addSbtPlugin("ch.epfl.lamp" % "sbt-dotty" % sys.props("plugin.version"))
diff --git a/sbt-dotty/sbt-test/source-dependencies/missing-annot/test b/sbt-dotty/sbt-test/source-dependencies/missing-annot/test
new file mode 100644
index 000000000000..1e8071204c47
--- /dev/null
+++ b/sbt-dotty/sbt-test/source-dependencies/missing-annot/test
@@ -0,0 +1,8 @@
+> a/compile
+$ mkdir b-input
+# Add A to the classpath of b but not the annotations referenced by the members of A
+$ copy-file a-output/A.class b-input/A.class
+$ copy-file a-output/A.tasty b-input/A.tasty
+# B should still be able to compile even though ExtractAPI forces the
+# annotations of all inherited members.
+> b/compile