diff --git a/docs/src/main/paradox/configuration.md b/docs/src/main/paradox/configuration.md
index c0a33c19..5188536a 100644
--- a/docs/src/main/paradox/configuration.md
+++ b/docs/src/main/paradox/configuration.md
@@ -29,12 +29,13 @@ If a file duplicate exist between the directories, the overlay file is dropped i
 
 ## Multi Configuration
 
-Paradox supports multiple sbt configurations. Each configuration is by default located to `src/configName` of the project,
-with the target directory defined as `target/paradox/site/configName`, `configName` corresponding to configuration.name of
-a particular configuration. There still remains the usual main project in `src/main` of course if you don't need multiple
-paradox project directories.
+By default, Paradox expects documentation source files in the `src/main/paradox` directory.
+For situations where different parts of the documentation are stored separately, Paradox supports custom sbt configuration scopes.
+Each custom configuration source files are by default located in the `src/<config-name>/paradox` directory.
+The target directory is defined as `target/paradox/site/<config-name>`.
+Here `<config-name>` corresponds to `configuration.name` of a particular configuration.
 
-To associate a configuration to paradox, use its settings, and change its default source and/or target directorie(s) if needed:
+To associate a configuration to paradox, manually add settings from `ParadoxPlugin.paradoxSettings`, and change its default source and/or target directories if needed:
 
 ```scala
 val SomeConfig = config("some-config")
@@ -49,7 +50,8 @@ lazy val root = (project in file(".")).
   )
 ```
 
-Now, either you run paradox on one configuration; "sbt someConfig:paradox" or you can run the main project with the usual way; "sbt paradox".
+Now, to run paradox for custom configuration execute `sbt someConfig:paradox`.
+It is still possible to run paradox for the main configuration the usual way `sbt paradox`.
 
 ## Version warning
 
diff --git a/plugin/src/main/scala/com/lightbend/paradox/sbt/ParadoxPlugin.scala b/plugin/src/main/scala/com/lightbend/paradox/sbt/ParadoxPlugin.scala
index dd2b9a91..b71d8374 100644
--- a/plugin/src/main/scala/com/lightbend/paradox/sbt/ParadoxPlugin.scala
+++ b/plugin/src/main/scala/com/lightbend/paradox/sbt/ParadoxPlugin.scala
@@ -114,7 +114,7 @@ object ParadoxPlugin extends AutoPlugin {
     excludeFilter in paradoxMarkdownToHtml := HiddenFileFilter,
     sources in paradoxMarkdownToHtml := Defaults.collectFiles(sourceDirectories in paradox, includeFilter in paradoxMarkdownToHtml, excludeFilter in paradoxMarkdownToHtml).value,
     mappings in paradoxMarkdownToHtml := Defaults.relativeMappings(sources in paradoxMarkdownToHtml, sourceDirectories in paradox).value,
-    target in paradoxMarkdownToHtml := target.value / "paradox" / "html",
+    target in paradoxMarkdownToHtml := target.value / "paradox" / "html" / configTarget(configuration.value),
 
     managedSourceDirectories in paradoxTheme := paradoxTheme.value.toSeq.map { theme =>
       (WebKeys.webJarsDirectory in Assets).value / (WebKeys.webModulesLib in Assets).value / theme.name
@@ -130,7 +130,7 @@ object ParadoxPlugin extends AutoPlugin {
     // if there are duplicates, select the file from the local template to allow overrides/extensions in themes
     WebKeys.deduplicators in paradoxTheme += SbtWeb.selectFileFrom((sourceDirectory in paradoxTheme).value),
     mappings in paradoxTheme := SbtWeb.deduplicateMappings((mappings in paradoxTheme).value, (WebKeys.deduplicators in paradoxTheme).value),
-    target in paradoxTheme := target.value / "paradox" / "theme",
+    target in paradoxTheme := target.value / "paradox" / "theme" / configTarget(configuration.value),
     paradoxThemeDirectory := SbtWeb.syncMappings(WCompat.cacheStore(streams.value, "paradox-theme"), (mappings in paradoxTheme).value, (target in paradoxTheme).value),
 
     paradoxTemplate := {
@@ -185,13 +185,7 @@ object ParadoxPlugin extends AutoPlugin {
       val themeFilter = (managedSourceDirectories in paradoxTheme).value.headOption.map(InDirectoryFilter).getOrElse(NothingFilter)
       (mappings in Assets).value filterNot { case (file, path) => themeFilter.accept(file) }
     },
-    target in paradox := {
-      val config = configuration.value
-      if (config.name != Compile.name)
-        target.value / "paradox" / "site" / config.name
-      else
-        target.value / "paradox" / "site" / "main"
-    },
+    target in paradox := target.value / "paradox" / "site" / configTarget(configuration.value),
 
     watchSources in Defaults.ConfigGlobal ++= Compat.sourcesFor((sourceDirectories in paradox).value),
 
@@ -200,6 +194,10 @@ object ParadoxPlugin extends AutoPlugin {
     paradox := SbtWeb.syncMappings(WCompat.cacheStore(streams.value, "paradox"), (mappings in paradox).value, (target in paradox).value)
   )
 
+  private def configTarget(config: Configuration) =
+    if (config.name == Compile.name) "main"
+    else config.name
+
   def shortVersion(version: String): String = version.replace("-SNAPSHOT", "*")
 
   def dateProperties: Map[String, String] = {
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/build.sbt b/plugin/src/sbt-test/paradox/custom-configuration/build.sbt
new file mode 100644
index 00000000..e40f762c
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/build.sbt
@@ -0,0 +1,23 @@
+val Docs1 = config("docs1")
+val Docs2 = config("docs2")
+
+enablePlugins(ParadoxPlugin)
+
+ParadoxPlugin.paradoxSettings(Docs1)
+ParadoxPlugin.paradoxSettings(Docs2)
+
+TaskKey[Unit]("makeDocs") := {
+  (Docs1 / paradox).value
+  (Docs2 / paradox).value
+}
+
+TaskKey[Unit]("check") := {
+  def checkFileContent(file: File, expected: String) = {
+    assert(file.exists, s"${file.getAbsolutePath} does not exists")
+    val contents = IO.readLines(file)
+    assert(contents.exists(_.contains(expected)), s"Did not find '$expected' in\n${contents.mkString("\n")}")
+  }
+
+  checkFileContent((Docs1 / paradox / target).value / "index.html", "Docs1 index")
+  checkFileContent((Docs2 / paradox / target).value / "index.html", "Docs2 index")
+}
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/project/build.properties b/plugin/src/sbt-test/paradox/custom-configuration/project/build.properties
new file mode 100644
index 00000000..c0bab049
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/project/build.properties
@@ -0,0 +1 @@
+sbt.version=1.2.8
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/project/plugins.sbt b/plugin/src/sbt-test/paradox/custom-configuration/project/plugins.sbt
new file mode 100644
index 00000000..be8b011a
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/project/plugins.sbt
@@ -0,0 +1 @@
+addSbtPlugin("com.lightbend.paradox" % "sbt-paradox" % sys.props("project.version"))
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/src/docs1/paradox/index.md b/plugin/src/sbt-test/paradox/custom-configuration/src/docs1/paradox/index.md
new file mode 100644
index 00000000..d7108780
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/src/docs1/paradox/index.md
@@ -0,0 +1 @@
+Docs1 index.
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/src/docs2/paradox/index.md b/plugin/src/sbt-test/paradox/custom-configuration/src/docs2/paradox/index.md
new file mode 100644
index 00000000..7a582ee8
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/src/docs2/paradox/index.md
@@ -0,0 +1 @@
+Docs2 index.
diff --git a/plugin/src/sbt-test/paradox/custom-configuration/test b/plugin/src/sbt-test/paradox/custom-configuration/test
new file mode 100644
index 00000000..0afa4704
--- /dev/null
+++ b/plugin/src/sbt-test/paradox/custom-configuration/test
@@ -0,0 +1,2 @@
+> makeDocs
+> check