diff --git a/src/main/scala/sbt/internal/ProjectMatrix.scala b/src/main/scala/sbt/internal/ProjectMatrix.scala
index 9c920d69d..cacb82596 100644
--- a/src/main/scala/sbt/internal/ProjectMatrix.scala
+++ b/src/main/scala/sbt/internal/ProjectMatrix.scala
@@ -499,7 +499,7 @@ object ProjectMatrix {
           acc.customRow(autoScalaLibrary, axisValues ++ Seq(VirtualAxis.scalaABIVersion(sv)), process)
         }
       } else {
-        customRow(autoScalaLibrary, Seq(VirtualAxis.jvm), process)
+        customRow(autoScalaLibrary, axisValues ++ Seq(VirtualAxis.jvm), process)
       }
 
     override def customRow(
diff --git a/src/sbt-test/projectMatrix/jvm-with-project-axes/build.sbt b/src/sbt-test/projectMatrix/jvm-with-project-axes/build.sbt
new file mode 100644
index 000000000..6d90cf48e
--- /dev/null
+++ b/src/sbt-test/projectMatrix/jvm-with-project-axes/build.sbt
@@ -0,0 +1,46 @@
+import sbt.internal.ProjectMatrix
+ThisBuild / organization := "com.example"
+ThisBuild / version := "0.1.0-SNAPSHOT"
+ThisBuild / publishMavenStyle := true
+
+ThisBuild / ivyPaths := {
+  val base = (ThisBuild / baseDirectory).value
+  IvyPaths(base, Some(base / "ivy-cache"))
+}
+publish / skip := true
+
+lazy val scala212 = "2.12.10"
+
+lazy val check = taskKey[Unit]("")
+
+lazy val config12 = ConfigAxis("Config1_2", "-config1.2")
+lazy val config13 = ConfigAxis("Config1_3", "-config1.3")
+
+check := {
+  val app12 = app.finder(config12).apply(autoScalaLibrary = false)
+  assert(app12.id == "appConfig1_2", s"app12.id is ${app12.id}")
+  val app13 = app.finder(config13).apply(autoScalaLibrary = false)
+  assert(app13.id == "appConfig1_3", s"app13.id is ${app13.id}")
+}
+
+lazy val app: ProjectMatrix = (projectMatrix in file("app"))
+  .settings(
+    name := "app",
+    ivyPaths := (ThisBuild / ivyPaths).value
+  )
+  .customRow(
+    autoScalaLibrary = false,
+    scalaVersions = Seq(scala212),
+    axisValues = Seq(config12, VirtualAxis.jvm),
+    _.settings(
+      libraryDependencies += "com.typesafe" % "config" % "1.2.1"
+    )
+  )
+  .customRow(
+    autoScalaLibrary = false,
+    scalaVersions = Seq(scala212),
+    axisValues = Seq(config13, VirtualAxis.jvm),
+    _.settings(
+      libraryDependencies += "com.typesafe" % "config" % "1.3.3"
+    )
+  )
diff --git a/src/sbt-test/projectMatrix/jvm-with-project-axes/project/ConfigAxis.scala b/src/sbt-test/projectMatrix/jvm-with-project-axes/project/ConfigAxis.scala
new file mode 100644
index 000000000..bdabcb757
--- /dev/null
+++ b/src/sbt-test/projectMatrix/jvm-with-project-axes/project/ConfigAxis.scala
@@ -0,0 +1,3 @@
+import sbt._
+
+case class ConfigAxis(idSuffix: String, directorySuffix: String) extends VirtualAxis.WeakAxis
diff --git a/src/sbt-test/projectMatrix/jvm-with-project-axes/project/plugins.sbt b/src/sbt-test/projectMatrix/jvm-with-project-axes/project/plugins.sbt
new file mode 100644
index 000000000..4e80bbafc
--- /dev/null
+++ b/src/sbt-test/projectMatrix/jvm-with-project-axes/project/plugins.sbt
@@ -0,0 +1,5 @@
+sys.props.get("plugin.version") match {
+  case Some(x) => addSbtPlugin("com.eed3si9n" % "sbt-projectmatrix" % x)
+  case _ => sys.error("""|The system property 'plugin.version' is not defined.
+                         |Specify this property using the scriptedLaunchOpts -D.""".stripMargin)
+}
diff --git a/src/sbt-test/projectMatrix/jvm-with-project-axes/test b/src/sbt-test/projectMatrix/jvm-with-project-axes/test
new file mode 100644
index 000000000..15675b169
--- /dev/null
+++ b/src/sbt-test/projectMatrix/jvm-with-project-axes/test
@@ -0,0 +1 @@
+> check