diff --git a/src/TulsiGenerator/DeploymentTarget.swift b/src/TulsiGenerator/DeploymentTarget.swift
index 13e9df6..68d91ba 100644
--- a/src/TulsiGenerator/DeploymentTarget.swift
+++ b/src/TulsiGenerator/DeploymentTarget.swift
@@ -146,6 +146,15 @@
     }
   }
 
+  var userString: String {
+    switch self {
+    case .ios: return "iOS"
+    case .macos: return "macOS"
+    case .tvos: return "tvOS"
+    case .watchos: return "watchOS"
+    }
+  }
+
   /// Path of where the test host is expected to be built for each available platform.
   func testHostPath(hostTargetPath: String, hostTargetProductName: String) -> String? {
     switch self {
diff --git a/src/TulsiGenerator/RuleEntryMap.swift b/src/TulsiGenerator/RuleEntryMap.swift
index 5020536..c91e01d 100644
--- a/src/TulsiGenerator/RuleEntryMap.swift
+++ b/src/TulsiGenerator/RuleEntryMap.swift
@@ -42,16 +42,7 @@
 
   public func insert(ruleEntry: RuleEntry) {
     allEntries.append(ruleEntry)
-
-    let label = ruleEntry.label
-    guard var entries = labelToEntries[label] else {
-      labelToEntries[label] = [ruleEntry]
-      return
-    }
-    // Don't warn about duplicate entries with the same DeploymentTarget as they should
-    // only be caused by a root-level library which we already warn about.
-    entries.append(ruleEntry)
-    labelToEntries[label] = entries
+    labelToEntries[ruleEntry.label, default: []].append(ruleEntry)
   }
 
   public func hasAnyRuleEntry(withBuildLabel buildLabel: BuildLabel) -> Bool {
diff --git a/src/TulsiGenerator/XcodeProjectGenerator.swift b/src/TulsiGenerator/XcodeProjectGenerator.swift
index 8e56234..0de351f 100644
--- a/src/TulsiGenerator/XcodeProjectGenerator.swift
+++ b/src/TulsiGenerator/XcodeProjectGenerator.swift
@@ -82,10 +82,6 @@
   private static let DefaultSwiftVersion = "4"
   private static let SupportScriptsPath = "Library/Application Support/Tulsi/Scripts"
 
-  /// Rules which should not be generated at the top level.
-  private static let LibraryRulesForTopLevelWarning =
-      Set(["objc_library", "swift_library", "cc_library"])
-
   private let workspaceRootURL: URL
   private let config: TulsiGeneratorConfig
   private let localizedMessageLogger: LocalizedMessageLogger
@@ -333,7 +329,7 @@
   }
 
   /// Validates that the aspect output contains all targets listed in the config file and that
-  /// there are no ambiguous top-level targets.
+  /// any bundled iOS targets use the same minimum OS version.
   private func validateConfigReferences(_ ruleEntryMap: RuleEntryMap) throws {
     let unresolvedLabels = config.buildTargetLabels.filter {
       !ruleEntryMap.hasAnyRuleEntry(withBuildLabel: $0)
@@ -341,13 +337,43 @@
     if !unresolvedLabels.isEmpty {
       throw ProjectGeneratorError.labelResolutionFailed(Set<BuildLabel>(unresolvedLabels))
     }
-    for label in config.buildTargetLabels {
-      if let entry = ruleEntryMap.anyRuleEntry(withBuildLabel: label),
-         XcodeProjectGenerator.LibraryRulesForTopLevelWarning.contains(entry.type) {
-        localizedMessageLogger.warning("TopLevelLibraryTarget",
-                                       comment: "Warning when a library target is used as a top level buildTarget. Target in %1$@, target type in %2$@.",
-                                       values: entry.label.description, entry.type)
+
+    var bundleEntriesByMinIos = [String: [RuleEntry]]()
+
+    // Phase 1: Collect all bundled iOS targets into a dictionary by their min iOS version.
+    //   - Explicitly ignore the ios_default_host target which may be outside of a user's project.
+    for entry in ruleEntryMap.allRuleEntries {
+      // Only inspect bundled targets - they will all have a product type.
+      guard entry.productType != nil else { continue }
+
+      // Ignore the `ios_default_host` target as it's outside of the user's project.
+      guard entry.label.targetName != "ios_default_host" else { continue }
+
+      // For now we only care about iOS targets. In the future we could expand this to handle
+      // others platforms as well.
+      guard let deploymentTarget = entry.deploymentTarget,
+        deploymentTarget.platform == .ios else { continue }
+
+      bundleEntriesByMinIos[deploymentTarget.osVersion, default: []].append(entry)
+    }
+
+    // Phase 2: Warning if they have multiple min iOS versions.
+    if bundleEntriesByMinIos.count > 1 {
+      let platform = PlatformType.ios.userString
+
+      // Sort the entries so the most popular min iOS version is first.
+      let sortedEntries = bundleEntriesByMinIos.enumerated().sorted { (a, b) -> Bool in
+        return a.element.value.count > b.element.value.count
       }
+      let debugString = sortedEntries.map { (offset, element) in
+        let targets = element.value.map { $0.label.value }.joined(separator: ", ")
+        return "\(platform) \(element.key) minimum_os_version: target(s) \(targets)"
+      }.joined(separator: "\n")
+
+      localizedMessageLogger.warning("MultiMinOSVersions",
+                                   comment: "Warning when multiple bundled targets have different minimum OS versions. Platform type in %1$@, context in %2$@.",
+                                   context: config.projectName,
+                                   values: platform, debugString)
     }
   }
 
diff --git a/src/TulsiGenerator/en.lproj/Localizable.strings b/src/TulsiGenerator/en.lproj/Localizable.strings
index cb85d0b..67e2d22 100644
--- a/src/TulsiGenerator/en.lproj/Localizable.strings
+++ b/src/TulsiGenerator/en.lproj/Localizable.strings
@@ -86,12 +86,12 @@
 /* Warning to show when a user has selected an XCTest but not its host application. */
 "MissingTestHost" = "Failed to link test target '%1$@' to its host, '%2$@'. This test will not be runnable in the generated Xcode project.";
 
+/* Warning when multiple bundled targets have different minimum OS versions. Platform type in %1$@, context in %2$@. */
+"MultiMinOSVersions" = "[ACTION REQUIRED] You have multiple top-level %1$@ bundle targets (e.g. applications or tests) with different minimum %1$@ versions.\nWe advise you to use a single minimum OS version for these targets in order to save Bazel analysis time and Xcode indexing time. You can fix this by setting a single `minimum_os_version` attribute on all of the targets mentioned below:\n------------------------\n%2$@\n------------------------";
+
 /* Warning to show when a RuleEntry does not have a DeploymentTarget to be used by the indexer. */
 "NoDeploymentTarget" = "Target %1$@ has no DeploymentTarget set. Defaulting to iOS 9. This is an unexpected problem and should be reported as a Tulsi bug.";
 
-/* Warning when a library target is used as a top level buildTarget. Target in %1$@, target type in %2$@. */
-"TopLevelLibraryTarget" = "You've included a %2$@ target (%1$@) in your project as a top-level build target. This is not supported and may trigger other warnings and errors. We advise you to no longer reference any %2$@ targets at the top level. Instead, use a top-level application or test target with %1$@ as a dependency.";
-
 /* Warning shown when none of the tests of a test suite %1$@ were able to be resolved. */
 "TestSuiteHasNoValidTests" = "Failed to resolve any tests for test_suite '%1$@', no scheme will be generated.";