diff --git a/src/main/scala/scalafix/sbt/ScalafixPlugin.scala b/src/main/scala/scalafix/sbt/ScalafixPlugin.scala
index 1f4cb6d0..1242584a 100644
--- a/src/main/scala/scalafix/sbt/ScalafixPlugin.scala
+++ b/src/main/scala/scalafix/sbt/ScalafixPlugin.scala
@@ -9,13 +9,13 @@ import sbt.*
 import sbt.internal.sbtscalafix.JLineAccess
 import sbt.internal.util.complete.Parser
 import sbt.plugins.JvmPlugin
+import sbt.librarymanagement.ResolveException
 import scalafix.interfaces.{ScalafixError, ScalafixMainCallback}
 import scalafix.internal.sbt.*
 
+import scala.annotation.nowarn
 import scala.collection.JavaConverters.collectionAsScalaIterableConverter
 import scala.util.control.NoStackTrace
-import sbt.librarymanagement.ResolveException
-
 import scala.util.Try
 
 object ScalafixPlugin extends AutoPlugin {
@@ -64,10 +64,15 @@ object ScalafixPlugin extends AutoPlugin {
         "Optional list of artifacts to resolve to run custom rules. " +
           "Can be set in ThisBuild or at project-level."
       )
+    @deprecated(
+      "scalafixScalaBinaryVersion now follows scalaBinaryVersion by default",
+      "0.12.1"
+    )
     val scalafixScalaBinaryVersion: SettingKey[String] =
       settingKey[String](
-        "The Scala binary version used for scalafix execution. Can be set in ThisBuild or at project-level. " +
-          "Custom rules must be compiled against that binary version. Defaults to 2.12."
+        "The Scala binary version used for scalafix execution. Must be set at project-level. " +
+          "Custom rules must be compiled against that binary version. Defaults to 2.12 for 2.12 projects, " +
+          "2.13 otherwise."
       )
     val scalafixConfig: SettingKey[Option[File]] =
       settingKey[Option[File]](
@@ -155,7 +160,7 @@ object ScalafixPlugin extends AutoPlugin {
         loadedRules = { () =>
           val scalafixInterface = ScalafixInterface(
             scalafixInterfaceCache.value,
-            scalafixScalaBinaryVersion.value,
+            scalafixScalaBinaryVersion.value: @nowarn,
             toolClasspath = Arg.ToolClasspath(
               // Local rules classpath must be looked up via tasks so they can't appear in completions
               Nil,
@@ -262,7 +267,13 @@ object ScalafixPlugin extends AutoPlugin {
       }
     },
     ivyConfigurations += ScalafixConfig,
-    scalafixAll := scalafixAllInputTask.evaluated
+    scalafixAll := scalafixAllInputTask.evaluated,
+    (scalafixScalaBinaryVersion: @nowarn) := {
+      scalaBinaryVersion.value match {
+        case "2.12" => "2.12"
+        case _ => "2.13"
+      }
+    }
   )
 
   override lazy val globalSettings: Seq[Def.Setting[_]] = Seq(
@@ -300,7 +311,6 @@ object ScalafixPlugin extends AutoPlugin {
           )
         }
       },
-      scalafixScalaBinaryVersion := "2.12",
       scalafixJGitCompletion := new JGitCompletion(baseDirectory.value.toPath)
     )
 
@@ -433,7 +443,7 @@ object ScalafixPlugin extends AutoPlugin {
         shellArgs,
         projectDepsExternal,
         projectDepsInternal,
-        scalafixScalaBinaryVersion.value,
+        scalafixScalaBinaryVersion.value: @nowarn,
         scalafixDependencies.value,
         allResolvers,
         (ThisBuild / scalafixCallback).value,
diff --git a/src/sbt-test/sbt-1.4/build-lint/build.sbt b/src/sbt-test/sbt-1.4/build-lint/build.sbt
index 8639100a..4e7833be 100644
--- a/src/sbt-test/sbt-1.4/build-lint/build.sbt
+++ b/src/sbt-test/sbt-1.4/build-lint/build.sbt
@@ -1,6 +1,5 @@
 ThisBuild / scalafixDependencies := Nil
 ThisBuild / scalafixResolvers := Nil
-ThisBuild / scalafixScalaBinaryVersion := "2.12"
 scalafixCaching := false
 scalafixConfig := None
 scalafixOnCompile := false
diff --git a/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-2.conf b/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-2.conf
new file mode 100644
index 00000000..3a228107
--- /dev/null
+++ b/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-2.conf
@@ -0,0 +1,2 @@
+rules = [OrganizeImports, ExplicitResultTypes]
+ExplicitResultTypes.skipSimpleDefinitions = false
\ No newline at end of file
diff --git a/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-3.conf b/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-3.conf
new file mode 100644
index 00000000..21c30ce0
--- /dev/null
+++ b/src/sbt-test/sbt-1.5/cross-build-scala3/.scalafix-3.conf
@@ -0,0 +1 @@
+rules = [OrganizeImports]
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/build.sbt b/src/sbt-test/sbt-1.5/cross-build-scala3/build.sbt
similarity index 62%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/build.sbt
rename to src/sbt-test/sbt-1.5/cross-build-scala3/build.sbt
index 29d01e99..eba0e41b 100644
--- a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/build.sbt
+++ b/src/sbt-test/sbt-1.5/cross-build-scala3/build.sbt
@@ -1,6 +1,6 @@
 import _root_.scalafix.sbt.{BuildInfo => Versions}
 
-val scala3Version = "3.3.0"
+val scala3Version = "3.4.1"
 ThisBuild / semanticdbEnabled := true
 ThisBuild / semanticdbVersion := scalafixSemanticdb.revision
 
@@ -13,12 +13,11 @@ lazy val root = project
       Versions.scala213,
       scala3Version
     ),
-    scalacOptions ++= (if (scalaVersion.value.startsWith("2"))
-                         Seq("-Ywarn-unused")
-                       else Seq()),
-    scalafixScalaBinaryVersion := {
-      if (scalaBinaryVersion.value == "3") scalafixScalaBinaryVersion.value
-      else scalaBinaryVersion.value
+    scalacOptions += {
+      if (scalaVersion.value.startsWith("2.12"))
+        "-Ywarn-unused-import"
+      else
+        "-Wunused:imports"
     },
     scalafixConfig := {
       if (scalaBinaryVersion.value == "3")
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/project/build.properties b/src/sbt-test/sbt-1.5/cross-build-scala3/project/build.properties
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/project/build.properties
rename to src/sbt-test/sbt-1.5/cross-build-scala3/project/build.properties
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/project/plugins.sbt b/src/sbt-test/sbt-1.5/cross-build-scala3/project/plugins.sbt
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/project/plugins.sbt
rename to src/sbt-test/sbt-1.5/cross-build-scala3/project/plugins.sbt
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-2/Main.scala b/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-2/Main.scala
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-2/Main.scala
rename to src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-2/Main.scala
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-2/Main.scala.expected b/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-2/Main.scala.expected
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-2/Main.scala.expected
rename to src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-2/Main.scala.expected
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-3/Main.scala b/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-3/Main.scala
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-3/Main.scala
rename to src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-3/Main.scala
diff --git a/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-3/Main.scala.expected b/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-3/Main.scala.expected
new file mode 100644
index 00000000..cb096903
--- /dev/null
+++ b/src/sbt-test/sbt-1.5/cross-build-scala3/src/main/scala-3/Main.scala.expected
@@ -0,0 +1,5 @@
+import scala.Int
+
+object Main {
+  def foo(a: Int) = a + 2.0f
+}
\ No newline at end of file
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/test b/src/sbt-test/sbt-1.5/cross-build-scala3/test
similarity index 100%
rename from src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/test
rename to src/sbt-test/sbt-1.5/cross-build-scala3/test
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-2.conf b/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-2.conf
deleted file mode 100644
index bbc1675b..00000000
--- a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-2.conf
+++ /dev/null
@@ -1,3 +0,0 @@
-rules = [DisableSyntax, OrganizeImports, ExplicitResultTypes]
-OrganizeImports.removeUnused = true
-ExplicitResultTypes.skipSimpleDefinitions = false
\ No newline at end of file
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-3.conf b/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-3.conf
deleted file mode 100644
index c2231433..00000000
--- a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/.scalafix-3.conf
+++ /dev/null
@@ -1,2 +0,0 @@
-rules = [DisableSyntax, OrganizeImports]
-OrganizeImports.removeUnused = false
\ No newline at end of file
diff --git a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-3/Main.scala.expected b/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-3/Main.scala.expected
deleted file mode 100644
index bf8fd25a..00000000
--- a/src/sbt-test/sbt-1.5/cross-build-scalafixScalaBinaryVersion/src/main/scala-3/Main.scala.expected
+++ /dev/null
@@ -1,7 +0,0 @@
-import scala.Int
-import scala.collection.AbstractSeq
-import scala.collection.Seq
-
-object Main {
-  def foo(a: Int) = a + 2.0f
-}
\ No newline at end of file
diff --git a/src/sbt-test/sbt-scalafix/local-rules/build.sbt b/src/sbt-test/sbt-scalafix/local-rules/build.sbt
index 1fef774b..03b7f94a 100644
--- a/src/sbt-test/sbt-scalafix/local-rules/build.sbt
+++ b/src/sbt-test/sbt-scalafix/local-rules/build.sbt
@@ -7,10 +7,7 @@ inThisBuild(
       "ch.epfl.scala" %% "example-scalafix-rule" % "1.4.0"
     ),
     resolvers += Resolver.sonatypeRepo("snapshots"),
-    scalaVersion := "2.13.11", // out of sync with scalafix.sbt.BuildInfo.scala213 on purpose
-    scalafixScalaBinaryVersion :=
-      // this should be the default in sbt-scalafix 1.0
-      CrossVersion.binaryScalaVersion(scalaVersion.value)
+    scalaVersion := "2.13.11" // out of sync with scalafix.sbt.BuildInfo.scala213 on purpose
   )
 )
 
diff --git a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/build.sbt b/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/build.sbt
deleted file mode 100644
index 21462e27..00000000
--- a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/build.sbt
+++ /dev/null
@@ -1,10 +0,0 @@
-import _root_.scalafix.sbt.{BuildInfo => V}
-
-inThisBuild(
-  List(
-    addCompilerPlugin(scalafixSemanticdb),
-    scalacOptions += "-Yrangepos",
-    scalaVersion := V.scala213,
-    scalafixScalaBinaryVersion := scalaBinaryVersion.value // this should be the default in sbt-scalafix 1.0
-  )
-)
diff --git a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/project/plugins.sbt b/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/project/plugins.sbt
deleted file mode 100644
index 2d3b4d3b..00000000
--- a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/project/plugins.sbt
+++ /dev/null
@@ -1,2 +0,0 @@
-resolvers += Resolver.sonatypeRepo("public")
-addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % sys.props("plugin.version"))
diff --git a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/src/main/scala/NeedExplicitResultTypes.scala b/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/src/main/scala/NeedExplicitResultTypes.scala
deleted file mode 100644
index 1da5a2da..00000000
--- a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/src/main/scala/NeedExplicitResultTypes.scala
+++ /dev/null
@@ -1,6 +0,0 @@
-object NeedExplicitResultTypes {
-  def a = {
-    println("foobar")
-    123
-  }
-}
diff --git a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/test b/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/test
deleted file mode 100644
index 06f59062..00000000
--- a/src/sbt-test/sbt-scalafix/scalafixScalaBinaryVersion/test
+++ /dev/null
@@ -1,5 +0,0 @@
-# ExplicitResultTypes uses the presentation compiler so the rule must run with the same scala binary version as the target
--> scalafix --check ExplicitResultTypes
-> scalafix ExplicitResultTypes
-> scalafix --check ExplicitResultTypes
-