diff --git a/librarymanagement/src/main/scala/sbt/internal/librarymanagement/Ivy.scala b/librarymanagement/src/main/scala/sbt/internal/librarymanagement/Ivy.scala
index 320f549a0..3198c95d0 100644
--- a/librarymanagement/src/main/scala/sbt/internal/librarymanagement/Ivy.scala
+++ b/librarymanagement/src/main/scala/sbt/internal/librarymanagement/Ivy.scala
@@ -168,7 +168,21 @@ final class IvySbt(val configuration: IvyConfiguration, fileToStore: File => Cac
             case pc: PomConfiguration      => configurePom(pc)
             case ifc: IvyFileConfiguration => configureIvyFile(ifc)
           }
-        moduleSettings.ivyScala.foreach(IvyScala.checkModule(baseModule, baseConfiguration, configuration.log))
+
+        val configs =
+          moduleSettings match {
+            case ic: InlineConfiguration             => ic.configurations
+            case ic: InlineConfigurationWithExcludes => ic.configurations
+            case ec: EmptyConfiguration              => Nil
+            case pc: PomConfiguration                => Configurations.default ++ Configurations.defaultInternal
+            case ifc: IvyFileConfiguration           => Configurations.default ++ Configurations.defaultInternal
+          }
+        moduleSettings.ivyScala match {
+          case Some(is) =>
+            val svc = configs.toVector filter Configurations.underScalaVersion map { _.name }
+            IvyScala.checkModule(baseModule, baseConfiguration, svc, configuration.log)(is)
+          case _ => // do nothing
+        }
         IvySbt.addExtraNamespace(baseModule)
         (baseModule, baseConfiguration)
       }
diff --git a/librarymanagement/src/main/scala/sbt/librarymanagement/ConfigurationExtra.scala b/librarymanagement/src/main/scala/sbt/librarymanagement/ConfigurationExtra.scala
index f3b267e24..8e30e5c6c 100644
--- a/librarymanagement/src/main/scala/sbt/librarymanagement/ConfigurationExtra.scala
+++ b/librarymanagement/src/main/scala/sbt/librarymanagement/ConfigurationExtra.scala
@@ -47,6 +47,15 @@ object Configurations {
   private[sbt] def DefaultConfiguration(mavenStyle: Boolean) = if (mavenStyle) DefaultMavenConfiguration else DefaultIvyConfiguration
   private[sbt] def defaultConfiguration(mavenStyle: Boolean) = if (mavenStyle) Configurations.Compile else Configurations.Default
   private[sbt] def removeDuplicates(configs: Iterable[Configuration]) = Set(scala.collection.mutable.Map(configs.map(config => (config.name, config)).toSeq: _*).values.toList: _*)
+
+  /** Returns true if the configuration should be under the influence of scalaVersion. */
+  private[sbt] def underScalaVersion(c: Configuration): Boolean =
+    c match {
+      case Default | Compile | IntegrationTest | Provided | Runtime | Test | Optional |
+        CompilerPlugin | CompileInternal | RuntimeInternal | TestInternal => true
+      case config =>
+        config.extendsConfigs exists underScalaVersion
+    }
 }
 
 abstract class ConfigurationExtra {
diff --git a/librarymanagement/src/main/scala/sbt/librarymanagement/IvyScalaExtra.scala b/librarymanagement/src/main/scala/sbt/librarymanagement/IvyScalaExtra.scala
index 39ecbace4..625c5e00f 100644
--- a/librarymanagement/src/main/scala/sbt/librarymanagement/IvyScalaExtra.scala
+++ b/librarymanagement/src/main/scala/sbt/librarymanagement/IvyScalaExtra.scala
@@ -47,24 +47,28 @@ import ScalaArtifacts._
 
 private[sbt] abstract class IvyScalaFunctions {
   /** Performs checks/adds filters on Scala dependencies (if enabled in IvyScala). */
-  def checkModule(module: DefaultModuleDescriptor, conf: String, log: Logger)(check: IvyScala): Unit = {
+  def checkModule(module: DefaultModuleDescriptor, conf: String, scalaVersionConfigs: Vector[String], log: Logger)(check: IvyScala): Unit = {
     if (check.checkExplicit)
       checkDependencies(module, check.scalaOrganization, check.scalaArtifacts, check.scalaBinaryVersion, check.configurations, log)
     if (check.filterImplicit)
       excludeScalaJars(module, check.configurations)
     if (check.overrideScalaVersion)
-      overrideScalaVersion(module, check.scalaOrganization, check.scalaFullVersion)
+      overrideScalaVersion(module, check.scalaOrganization, check.scalaFullVersion, scalaVersionConfigs)
   }
 
-  class OverrideScalaMediator(scalaOrganization: String, scalaVersion: String) extends DependencyDescriptorMediator {
+  class OverrideScalaMediator(scalaOrganization: String, scalaVersion: String, scalaVersionConfigs0: Vector[String]) extends DependencyDescriptorMediator {
+    private[this] val scalaVersionConfigs = scalaVersionConfigs0.toSet
     def mediate(dd: DependencyDescriptor): DependencyDescriptor = {
+      // Mediate only for the dependencies in scalaVersion configurations. https://github.com/sbt/sbt/issues/2786
+      def configQualifies: Boolean =
+        (dd.getModuleConfigurations exists { scalaVersionConfigs })
       val transformer =
         new NamespaceTransformer {
           def transform(mrid: ModuleRevisionId): ModuleRevisionId = {
             if (mrid == null) mrid
             else
               mrid.getName match {
-                case name @ (CompilerID | LibraryID | ReflectID | ActorsID | ScalapID) =>
+                case name @ (CompilerID | LibraryID | ReflectID | ActorsID | ScalapID) if configQualifies =>
                   ModuleRevisionId.newInstance(scalaOrganization, name, mrid.getBranch, scalaVersion, mrid.getQualifiedExtraAttributes)
                 case _ => mrid
               }
@@ -77,8 +81,8 @@ private[sbt] abstract class IvyScalaFunctions {
     }
   }
 
-  def overrideScalaVersion(module: DefaultModuleDescriptor, organization: String, version: String): Unit = {
-    val mediator = new OverrideScalaMediator(organization, version)
+  def overrideScalaVersion(module: DefaultModuleDescriptor, organization: String, version: String, scalaVersionConfigs: Vector[String]): Unit = {
+    val mediator = new OverrideScalaMediator(organization, version, scalaVersionConfigs)
     module.addDependencyDescriptorMediator(new ModuleId(Organization, "*"), ExactPatternMatcher.INSTANCE, mediator)
     if (organization != Organization)
       module.addDependencyDescriptorMediator(new ModuleId(organization, "*"), ExactPatternMatcher.INSTANCE, mediator)