diff --git a/modules/codegen-plugin/src/sbt-test/codegen-plugin/custom-settings/build.sbt b/modules/codegen-plugin/src/sbt-test/codegen-plugin/custom-settings/build.sbt
index 8b4c80ea7..5377ed157 100644
--- a/modules/codegen-plugin/src/sbt-test/codegen-plugin/custom-settings/build.sbt
+++ b/modules/codegen-plugin/src/sbt-test/codegen-plugin/custom-settings/build.sbt
@@ -1,6 +1,8 @@
 lazy val commonSettings = Def.settings(
   scalaVersion := "2.13.6",
-  Compile / smithy4sInputDir := (ThisBuild / baseDirectory).value / "smithy_input",
+  Compile / smithy4sInputDirs := Seq(
+    (ThisBuild / baseDirectory).value / "smithy_input"
+  ),
   Compile / smithy4sAllowedNamespaces := List(
     "aws.iam",
     "smithy4s.example"
diff --git a/modules/codegen-plugin/src/smithy4s/codegen/Smithy4sCodegenPlugin.scala b/modules/codegen-plugin/src/smithy4s/codegen/Smithy4sCodegenPlugin.scala
index 8569bb2d2..9102af081 100644
--- a/modules/codegen-plugin/src/smithy4s/codegen/Smithy4sCodegenPlugin.scala
+++ b/modules/codegen-plugin/src/smithy4s/codegen/Smithy4sCodegenPlugin.scala
@@ -33,10 +33,9 @@ object Smithy4sCodegenPlugin extends AutoPlugin {
     val smithy4sVersion =
       settingKey[String]("Smithy4sVersion")
 
-    val smithy4sInputDir =
-      settingKey[File](
-        "Input directory for smithy specs (.smithy or .json files)"
-      )
+    val smithy4sInputDirs = settingKey[Seq[File]](
+      "Input directories for smithy specs (.smithy or .json files)"
+    )
 
     val smithy4sOutputDir =
       settingKey[File](
@@ -98,7 +97,8 @@ object Smithy4sCodegenPlugin extends AutoPlugin {
 
   // Use this with any configuration to enable the codegen in it.
   def defaultSettings(config: Configuration) = Seq(
-    config / smithy4sInputDir := (config / sourceDirectory).value / "smithy",
+    config / smithy4sInputDirs := (config / unmanagedSourceDirectories).value
+      .map(_.getParentFile() / "smithy"),
     config / smithy4sOutputDir := (config / sourceManaged).value,
     config / smithy4sResourceDir := (config / resourceManaged).value,
     config / smithy4sCodegen := cachedSmithyCodegen(config).value,
@@ -139,7 +139,7 @@ object Smithy4sCodegenPlugin extends AutoPlugin {
 
   def cachedSmithyCodegen(conf: Configuration) = Def.task {
     val inputFiles =
-      Option((conf / smithy4sInputDir).value)
+      Option((conf / smithy4sInputDirs).value).toSeq.flatten
         .filter(_.exists())
         .toList
     val outputPath = (conf / smithy4sOutputDir).value
diff --git a/modules/docs/markdown/01-overview/03-installation.md b/modules/docs/markdown/01-overview/03-installation.md
index 34f9bfbc2..d210d3311 100644
--- a/modules/docs/markdown/01-overview/03-installation.md
+++ b/modules/docs/markdown/01-overview/03-installation.md
@@ -31,7 +31,7 @@ val myModule = project
 
 This will enable the plugin on `myModule`. We also need to add `smithy4s-core ` here since it is needed for compiling the generated code.
 
-By default, the plugin will look in the `$MY_MODULE/src/main/smithy` directory and will write scala code in `$MY_MODULE/target/scala-<version>/src_managed/` when invoking `compile`. The paths are configurable via the `smithy4sInputDir` and `smithy4sOutputDir` settings keys.
+By default, the plugin will look in the `$MY_MODULE/src/main/smithy` directory and will write scala code in `$MY_MODULE/target/scala-<version>/src_managed/` when invoking `compile`. The paths are configurable via the `smithy4sInputDirs` and `smithy4sOutputDir` settings keys.
 
 For example, in order for the plugin to source `.smithy` specs from `./smithy_input` (inside the folder where our `build.sbt` is) and output the generated files into `./smithy_output`.
 
@@ -41,8 +41,8 @@ val myModule = project
   .enablePlugins(Smithy4sCodegenPlugin)
   .settings(
     scalaVersion := "@SCALA_VERSION@",
-    smithy4sInputDir in Compile  := (ThisBuild / baseDirectory).value / "smithy_input",
-    smithy4sOutputDir in Compile := (ThisBuild / baseDirectory).value / "smithy_output",
+    Compile / smithy4sInputDirs := Seq((ThisBuild / baseDirectory).value / "smithy_input"),
+    Compile / smithy4sOutputDir := (ThisBuild / baseDirectory).value / "smithy_output",
     libraryDependencies += "com.disneystreaming.smithy4s" %% "smithy4s-core" % smithy4sVersion.value
   )
 ```
@@ -66,7 +66,7 @@ object example extends ScalaModule with Smithy4sModule {
 }
 ```
 
-By default, the `mill` plugin will look for Smithy files under the `$MY_MODULE/smithy` directory. The generated code ends up in `out/$MY_MODULE/smithy4sOutputDir.dest/scala/`, again, by default. Code generation happens automatically when you before you `compile` the module. The paths are configurable via the `smithy4sInputDir` and `smithy4sOutputDir` tasks.
+By default, the `mill` plugin will look for Smithy files under the `$MY_MODULE/smithy` directory. The generated code ends up in `out/$MY_MODULE/smithy4sOutputDir.dest/scala/`, again, by default. Code generation happens automatically when you before you `compile` the module. The paths are configurable via the `smithy4sInputDirs` and `smithy4sOutputDir` tasks.
 
 For example, here we'll read Smithy files from `smithy_input` and write to `smithy_output`.
 
@@ -81,8 +81,8 @@ object example extends ScalaModule with Smithy4sModule {
     ivy"com.disneystreaming.smithy4s::smithy4s-core:${smithy4sVersion()}"
   )
 
-  override def smithy4sInputDir = T.source {
-    PathRef(T.ctx().workspace / "smithy_input")
+  override def smithy4sInputDirs = T.sources {
+    Seq(PathRef(T.ctx().workspace / "smithy_input"))
   }
   override def smithy4sOutputDir = T {
     PathRef(T.ctx().workspace / "smithy_output")
diff --git a/modules/mill-codegen-plugin/src/smithy4s/codegen/mill/Smithy4sModule.scala b/modules/mill-codegen-plugin/src/smithy4s/codegen/mill/Smithy4sModule.scala
index d47c6ef47..f8f71e03b 100644
--- a/modules/mill-codegen-plugin/src/smithy4s/codegen/mill/Smithy4sModule.scala
+++ b/modules/mill-codegen-plugin/src/smithy4s/codegen/mill/Smithy4sModule.scala
@@ -19,7 +19,7 @@ package smithy4s.codegen.mill
 import coursier.maven.MavenRepository
 import mill._
 import mill.api.PathRef
-import mill.define.Source
+import mill.define.Sources
 import mill.scalalib._
 import smithy4s.codegen.{CodegenArgs, Codegen => Smithy4s, FileType}
 import smithy4s.codegen.BuildInfo
@@ -27,8 +27,8 @@ import smithy4s.codegen.BuildInfo
 trait Smithy4sModule extends ScalaModule {
 
   /** Input directory for .smithy files */
-  protected def smithy4sInputDir: Source = T.source {
-    PathRef(millSourcePath / "smithy")
+  protected def smithy4sInputDirs: Sources = T.sources {
+    Seq(PathRef(millSourcePath / "smithy"))
   }
 
   protected def smithy4sOutputDir: T[PathRef] = T {
@@ -85,7 +85,7 @@ trait Smithy4sModule extends ScalaModule {
 
   def smithy4sCodegen: T[(PathRef, PathRef)] = T {
 
-    val specFiles = List(smithy4sInputDir().path).filter(os.exists(_))
+    val specFiles = smithy4sInputDirs().map(_.path).filter(os.exists(_))
 
     val scalaOutput = smithy4sOutputDir().path
     val resourcesOutput = smithy4sResourceOutputDir().path