diff --git a/metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/StandaloneMcpService.scala b/metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/StandaloneMcpService.scala
index 90085b6e34a..bfbcfc33a2f 100644
--- a/metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/StandaloneMcpService.scala
+++ b/metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/StandaloneMcpService.scala
@@ -63,7 +63,8 @@ class StandaloneMcpService(
   private val time: Time = Time.system
 
   private val clientConfig: ClientConfiguration = ClientConfiguration(
-    MetalsServerConfig.default
+    MetalsServerConfig.default,
+    NoopFeatureFlagProvider,
   )
 
   private val mcpClient = new ConfiguredLanguageClient(
diff --git a/metals-mcp/src/main/scala/scala/meta/metals/McpMain.scala b/metals-mcp/src/main/scala/scala/meta/metals/McpMain.scala
index 4a3b2063118..377d93ddcf9 100644
--- a/metals-mcp/src/main/scala/scala/meta/metals/McpMain.scala
+++ b/metals-mcp/src/main/scala/scala/meta/metals/McpMain.scala
@@ -8,6 +8,7 @@ import scala.concurrent.ExecutionContext
 import scala.concurrent.ExecutionContextExecutorService
 import scala.util.control.NonFatal
 
+import scala.meta.internal.infra.NoopFeatureFlagProvider
 import scala.meta.internal.metals.BuildInfo
 import scala.meta.internal.metals.ClientConfiguration
 import scala.meta.internal.metals.MetalsServerConfig
@@ -329,7 +330,8 @@ object McpMain {
         json.addProperty(k, v)
       }
     }
-    val clientConfiguration = ClientConfiguration(MetalsServerConfig.default)
+    val clientConfiguration =
+      ClientConfiguration(MetalsServerConfig.default, NoopFeatureFlagProvider)
     UserConfiguration.fromJson(json, clientConfiguration)
   }
 }
diff --git a/metals/src/main/scala/scala/meta/internal/metals/ClientConfiguration.scala b/metals/src/main/scala/scala/meta/internal/metals/ClientConfiguration.scala
index 18dad4ba1f5..378c1f47d56 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/ClientConfiguration.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/ClientConfiguration.scala
@@ -1,5 +1,8 @@
 package scala.meta.internal.metals
 
+import scala.meta.infra.FeatureFlagProvider
+import scala.meta.internal.infra.NoopFeatureFlagProvider
+import scala.meta.internal.metals.Configs.DefinitionIndexStrategy
 import scala.meta.internal.metals.Configs.GlobSyntaxConfig
 import scala.meta.internal.metals.config.DoctorFormat
 import scala.meta.internal.metals.config.StatusBarState
@@ -19,6 +22,7 @@ import org.eclipse.lsp4j.InitializeParams
 final class ClientConfiguration(
     val initialConfig: MetalsServerConfig,
     initializeParams: Option[InitializeParams],
+    featureFlags: FeatureFlagProvider,
 ) {
 
   private val clientCapabilities: Option[ClientCapabilities] =
@@ -67,6 +71,14 @@ final class ClientConfiguration(
       .flatMap(GlobSyntaxConfig.fromString)
       .getOrElse(initialConfig.globSyntax)
 
+  def definitionIndexStrategy(): DefinitionIndexStrategy =
+    DefinitionIndexStrategy
+      .fromConfigOrFeatureFlag(
+        initializationOptions.definitionIndexStrategy,
+        featureFlags,
+      )
+      .getOrElse(DefinitionIndexStrategy.default)
+
   def renameFileThreshold(): Int =
     initializationOptions.renameFileThreshold.getOrElse(
       initialConfig.renameFileThreshold
@@ -238,18 +250,21 @@ final class ClientConfiguration(
 }
 
 object ClientConfiguration {
-  val default: ClientConfiguration = ClientConfiguration(MetalsServerConfig())
+  val default: ClientConfiguration =
+    ClientConfiguration(MetalsServerConfig(), NoopFeatureFlagProvider)
 
   def apply(
       initialConfig: MetalsServerConfig,
       initializeParams: InitializeParams,
+      featureFlags: FeatureFlagProvider,
   ): ClientConfiguration = {
-    new ClientConfiguration(initialConfig, Some(initializeParams))
+    new ClientConfiguration(initialConfig, Some(initializeParams), featureFlags)
   }
 
   def apply(
-      initialConfig: MetalsServerConfig
+      initialConfig: MetalsServerConfig,
+      featureFlags: FeatureFlagProvider,
   ): ClientConfiguration = {
-    new ClientConfiguration(initialConfig, None)
+    new ClientConfiguration(initialConfig, None, featureFlags)
   }
 }
diff --git a/metals/src/main/scala/scala/meta/internal/metals/Configs.scala b/metals/src/main/scala/scala/meta/internal/metals/Configs.scala
index 272608b8094..5fc3869a6f6 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/Configs.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/Configs.scala
@@ -389,8 +389,7 @@ object Configs {
     // which fails on syntax errors. See plans/protopc.md for details.
     def default: ProtoOutlineProviderConfig = v1
     def fromConfigOrFeatureFlag(
-        value: Option[String],
-        featureFlags: FeatureFlagProvider,
+        value: Option[String]
     ): Either[String, ProtoOutlineProviderConfig] = {
       value match {
         case Some(ok @ ("v1" | "v2")) =>
diff --git a/metals/src/main/scala/scala/meta/internal/metals/Indexer.scala b/metals/src/main/scala/scala/meta/internal/metals/Indexer.scala
index cc1f0bf3be2..423341cce57 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/Indexer.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/Indexer.scala
@@ -248,7 +248,7 @@ case class Indexer(indexProviders: IndexProviders, mbtBuild: () => MbtBuild)(
         )
         progress.message =
           s"indexing ${buildTool.importedBuild.dependencyModules.getItems().size()} dependencies"
-        if (indexProviders.userConfig.definitionIndexStrategy.isClasspath) {
+        if (indexProviders.clientConfig.definitionIndexStrategy().isClasspath) {
           usedJars ++= indexDependencyModules(
             buildTool.importedBuild.dependencyModules,
             progress,
@@ -546,7 +546,9 @@ case class Indexer(indexProviders: IndexProviders, mbtBuild: () => MbtBuild)(
       if (!path.exists) {
         scribe.warn(s"dependency missing at absolute path: $path")
       } else if (path.isJar) {
-        if (!indexProviders.userConfig.definitionIndexStrategy.isClasspath) {
+        if (
+          !indexProviders.clientConfig.definitionIndexStrategy().isClasspath
+        ) {
           usedJars += path
           if (addSourceJarSymbols(path)) cacheHits += 1
           else cacheMisses += 1
diff --git a/metals/src/main/scala/scala/meta/internal/metals/InitializationOptions.scala b/metals/src/main/scala/scala/meta/internal/metals/InitializationOptions.scala
index f7372457a4a..bcc149572b2 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/InitializationOptions.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/InitializationOptions.scala
@@ -50,6 +50,8 @@ import org.eclipse.{lsp4j => l}
  *                            the output, you can enable this to strip them.
  * @param doctorVisibilityProvider if the clients implements `metals/doctorVisibilityDidChange`
  * @param bspStatusBarProvider if the client supports `metals/status` with "bsp" status type
+ * @param definitionIndexStrategy whether definitions from dependencies should index classfiles
+ *                                or source files.
  */
 final case class InitializationOptions(
     compilerOptions: CompilerInitializationOptions,
@@ -82,6 +84,7 @@ final case class InitializationOptions(
     doctorVisibilityProvider: Option[Boolean],
     bspStatusBarProvider: Option[String],
     moduleStatusBarProvider: Option[String],
+    definitionIndexStrategy: Option[String],
 ) {
   def doctorFormat: Option[DoctorFormat.DoctorFormat] =
     doctorProvider.flatMap(DoctorFormat.fromString)
@@ -128,6 +131,7 @@ object InitializationOptions {
     None,
     None,
     None,
+    None,
   )
 
   def from(
@@ -188,6 +192,8 @@ object InitializationOptions {
       bspStatusBarProvider = jsonObj.getStringOption("bspStatusBarProvider"),
       moduleStatusBarProvider =
         jsonObj.getStringOption("moduleStatusBarProvider"),
+      definitionIndexStrategy =
+        jsonObj.getStringOption("definitionIndexStrategy"),
     )
   }
 
diff --git a/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala b/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
index d967282bbeb..75d166c34a4 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
@@ -2397,7 +2397,7 @@ abstract class MetalsLspService(
       },
       toIndexSource = path => sourceMapper.mappedTo(path).getOrElse(path),
       isClasspathDefinitionIndexEnabled = () =>
-        userConfig.definitionIndexStrategy.isClasspath,
+        clientConfig.definitionIndexStrategy().isClasspath,
       mtags = () => mtags,
     )
   }
diff --git a/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala b/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
index 37721afbeb0..72be52a2de8 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
@@ -14,7 +14,6 @@ import scala.meta.internal.infra.NoopFeatureFlagProvider
 import scala.meta.internal.metals.Configs.AdditionalPcChecksConfig
 import scala.meta.internal.metals.Configs.BatchSemanticdbConfig
 import scala.meta.internal.metals.Configs.CompilerProgressConfig
-import scala.meta.internal.metals.Configs.DefinitionIndexStrategy
 import scala.meta.internal.metals.Configs.DefinitionProviderConfig
 import scala.meta.internal.metals.Configs.FallbackClasspathConfig
 import scala.meta.internal.metals.Configs.FallbackSourcepathConfig
@@ -99,8 +98,6 @@ case class UserConfiguration(
       WorkspaceSymbolProviderConfig.default,
     definitionProviders: DefinitionProviderConfig =
       DefinitionProviderConfig.default,
-    definitionIndexStrategy: DefinitionIndexStrategy =
-      DefinitionIndexStrategy.default,
     protoOutlineProvider: ProtoOutlineProviderConfig =
       ProtoOutlineProviderConfig.default,
     javaSymbolLoader: JavaSymbolLoaderConfig = JavaSymbolLoaderConfig.default,
@@ -275,12 +272,6 @@ case class UserConfiguration(
             definitionProviders.values.asJava,
           )
         ),
-        Some(
-          (
-            "definitionIndexStrategy",
-            definitionIndexStrategy.value,
-          )
-        ),
         Some(
           (
             "protoOutlineProvider",
@@ -1358,14 +1349,6 @@ object UserConfiguration {
           featureFlags,
         ),
     ).getOrElse(WorkspaceSymbolProviderConfig.default)
-    val definitionIndexStrategy = getParsedKey(
-      "definition-index-strategy",
-      value =>
-        DefinitionIndexStrategy.fromConfigOrFeatureFlag(
-          value,
-          featureFlags,
-        ),
-    ).getOrElse(DefinitionIndexStrategy.default)
     val definitionProviders = getParsedArrayKey(
       "definition-providers",
       values =>
@@ -1378,8 +1361,7 @@ object UserConfiguration {
       "proto-outline-provider",
       value =>
         ProtoOutlineProviderConfig.fromConfigOrFeatureFlag(
-          value,
-          featureFlags,
+          value
         ),
     ).getOrElse(ProtoOutlineProviderConfig.default)
     val javaSymbolLoader = getParsedKey(
@@ -1521,7 +1503,6 @@ object UserConfiguration {
           useSourcePath,
           workspaceSymbolProvider,
           definitionProviders,
-          definitionIndexStrategy,
           protoOutlineProvider,
           javaSymbolLoader,
           javaTurbineRecompileDelay,
diff --git a/metals/src/main/scala/scala/meta/internal/metals/WorkspaceLspService.scala b/metals/src/main/scala/scala/meta/internal/metals/WorkspaceLspService.scala
index b22ccd4376a..25e917624dd 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/WorkspaceLspService.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/WorkspaceLspService.scala
@@ -140,6 +140,7 @@ class WorkspaceLspService(
     ClientConfiguration(
       serverInputs.initialServerConfig,
       initializeParams,
+      featureFlags,
     )
 
   private val languageClient = {
diff --git a/tests/unit/src/main/scala/tests/BaseLspSuite.scala b/tests/unit/src/main/scala/tests/BaseLspSuite.scala
index 44e15b2b283..133c16ad62a 100644
--- a/tests/unit/src/main/scala/tests/BaseLspSuite.scala
+++ b/tests/unit/src/main/scala/tests/BaseLspSuite.scala
@@ -51,7 +51,6 @@ abstract class BaseLspSuite(
       buildChangedAction = BuildChangedAction.prompt,
       fallbackScalaVersion = Some(BuildInfo.scalaVersion),
       presentationCompilerDiagnostics = false,
-      definitionIndexStrategy = Configs.DefinitionIndexStrategy.classpath,
 
       // Legacy settings that are enabled for tests only.  We  should eventually
       // update the tests to use the new defaults.
diff --git a/tests/unit/src/test/scala/tests/CompletionLspSuite.scala b/tests/unit/src/test/scala/tests/CompletionLspSuite.scala
index 662bb50edba..926d82f34e7 100644
--- a/tests/unit/src/test/scala/tests/CompletionLspSuite.scala
+++ b/tests/unit/src/test/scala/tests/CompletionLspSuite.scala
@@ -3,7 +3,7 @@ package tests
 import scala.concurrent.Future
 
 import scala.meta.internal.metals.Configs.DefinitionIndexStrategy
-import scala.meta.internal.metals.UserConfiguration
+import scala.meta.internal.metals.InitializationOptions
 import scala.meta.internal.metals.{BuildInfo => V}
 
 import munit.Location
@@ -12,8 +12,11 @@ class CompletionLspSuite extends BaseCompletionLspSuite("completion") {
 
   override def munitIgnore: Boolean = isWindows
 
-  override def userConfig: UserConfiguration = super.userConfig
-    .copy(definitionIndexStrategy = DefinitionIndexStrategy.sources)
+  override def initializationOptions: Option[InitializationOptions] = Some(
+    InitializationOptions.Default.copy(
+      definitionIndexStrategy = Some(DefinitionIndexStrategy.sources.value)
+    )
+  )
 
   test("basic-213") {
     basicTest(V.scala213)
diff --git a/tests/unit/src/test/scala/tests/ManualSuite.scala b/tests/unit/src/test/scala/tests/ManualSuite.scala
index cd6a9aef51d..0faf860eec0 100644
--- a/tests/unit/src/test/scala/tests/ManualSuite.scala
+++ b/tests/unit/src/test/scala/tests/ManualSuite.scala
@@ -18,7 +18,6 @@ class ManualSuite extends BaseManualSuite {
       workspaceSymbolProvider = WorkspaceSymbolProviderConfig.mbt,
       javaSymbolLoader = JavaSymbolLoaderConfig.turbineClasspath,
       presentationCompilerDiagnostics = true,
-      definitionIndexStrategy = DefinitionIndexStrategy.classpath,
       fallbackSourcepath = FallbackSourcepathConfig.allSources,
       compilerProgress = CompilerProgressConfig.enabled,
       referenceProvider = ReferenceProviderConfig.mbt,
diff --git a/tests/unit/src/test/scala/tests/UserConfigurationSuite.scala b/tests/unit/src/test/scala/tests/UserConfigurationSuite.scala
index 7a32c01c173..901f35730ea 100644
--- a/tests/unit/src/test/scala/tests/UserConfigurationSuite.scala
+++ b/tests/unit/src/test/scala/tests/UserConfigurationSuite.scala
@@ -6,6 +6,7 @@ import java.util.Properties
 
 import scala.meta.infra.FeatureFlag
 import scala.meta.infra.FeatureFlagProvider
+import scala.meta.internal.infra.NoopFeatureFlagProvider
 import scala.meta.internal.metals.AutoImportBuildKind
 import scala.meta.internal.metals.BloopJvmProperties
 import scala.meta.internal.metals.ClientConfiguration
@@ -494,7 +495,6 @@ class UserConfigurationSuite extends BaseSuite {
     "mbt",
     "protobuf"
   ],
-  "definitionIndexStrategy": "classpath",
   "protoOutlineProvider": "v1",
   "javaSymbolLoader": "turbine-classpath",
   "javaTurbineRecompileDelay": "100 milliseconds",
@@ -533,7 +533,11 @@ class UserConfigurationSuite extends BaseSuite {
       Map("testExplorerProvider" -> true).asJava.toJsonObject
     )
 
-    val clientConfig = ClientConfiguration(MetalsServerConfig.default, params)
+    val clientConfig = ClientConfiguration(
+      MetalsServerConfig.default,
+      params,
+      NoopFeatureFlagProvider,
+    )
 
     val roundtrip = UserConfiguration
       .fromJson(