diff --git a/Sources/SwiftDocC/Infrastructure/DocumentationContext.swift b/Sources/SwiftDocC/Infrastructure/DocumentationContext.swift
index 83a9aabba..83a94dc89 100644
--- a/Sources/SwiftDocC/Infrastructure/DocumentationContext.swift
+++ b/Sources/SwiftDocC/Infrastructure/DocumentationContext.swift
@@ -1317,6 +1317,22 @@ public class DocumentationContext {
                 uniqueRelationships.formUnion(unifiedSymbolGraph.orphanRelationships)
             }
             
+            // Warn when the documentation contains more than one main module
+            if moduleReferences.count > 1 {
+                let diagnostic = Diagnostic(
+                    source: nil,
+                    severity: .warning,
+                    range: nil,
+                    identifier: "org.swift.docc.MultipleMainModules",
+                    summary: "Documentation contains more than one main module",
+                    explanation: """
+                    The documentation inputs contain symbol graphs for more than one main module: \(moduleReferences.keys.sorted().joined(separator: ", ")).
+                    This may lead to unexpected behaviors in the generated documentation.
+                    """
+                )
+                diagnosticEngine.emit(Problem(diagnostic: diagnostic))
+            }
+            
             try shouldContinueRegistration()
             
             // Only add the symbol mapping now if the path hierarchy based resolver is the main implementation.
@@ -2309,6 +2325,38 @@ public class DocumentationContext {
         let (tutorialTableOfContentsResults, tutorials, tutorialArticles, allArticles, documentationExtensions) = result
         var (otherArticles, rootPageArticles) = splitArticles(allArticles)
         
+        // Warn when the documentation contains more than one root page
+        if rootPageArticles.count > 1 {
+            let extraRootPageProblems = rootPageArticles.map { rootPageArticle -> Problem in
+                let diagnostic = Diagnostic(
+                    source: rootPageArticle.source,
+                    severity: .warning,
+                    range: rootPageArticle.value.metadata?.technologyRoot?.originalMarkup.range,
+                    identifier: "org.swift.docc.MultipleTechnologyRoots",
+                    summary: "Documentation contains more than one root page",
+                    explanation: """
+                    The documentation contains \(rootPageArticles.count) articles with \(TechnologyRoot.directiveName.singleQuoted) directives.
+                    Only one article should be marked as a technology root to avoid unexpected behaviors.
+                    """
+                )
+                
+                guard let range = rootPageArticle.value.metadata?.technologyRoot?.originalMarkup.range else {
+                    return Problem(diagnostic: diagnostic)
+                }
+                
+                let solution = Solution(
+                    summary: "Remove the \(TechnologyRoot.directiveName.singleQuoted) directive",
+                    replacements: [
+                        Replacement(range: range, replacement: "")
+                    ]
+                )
+                
+                return Problem(diagnostic: diagnostic, possibleSolutions: [solution])
+            }
+            
+            diagnosticEngine.emit(extraRootPageProblems)
+        }
+        
         let globalOptions = (allArticles + documentationExtensions).compactMap { article in
             return article.value.options[.global]
         }
diff --git a/Tests/SwiftDocCTests/Infrastructure/DocumentationContext/DocumentationContext+RootPageTests.swift b/Tests/SwiftDocCTests/Infrastructure/DocumentationContext/DocumentationContext+RootPageTests.swift
index 9523dc096..5b73d1b1c 100644
--- a/Tests/SwiftDocCTests/Infrastructure/DocumentationContext/DocumentationContext+RootPageTests.swift
+++ b/Tests/SwiftDocCTests/Infrastructure/DocumentationContext/DocumentationContext+RootPageTests.swift
@@ -169,4 +169,175 @@ class DocumentationContext_RootPageTests: XCTestCase {
         
         XCTAssertEqual(context.problems.count, 0)
     }
+    
+    func testWarnsAboutMultipleTechnologyRootDirectives() async throws {
+        let (_, context) = try await loadBundle(catalog:
+            Folder(name: "multiple-roots.docc", content: [
+                TextFile(name: "FirstRoot.md", utf8Content: """
+                # First Root
+                @Metadata {
+                   @TechnologyRoot
+                }
+                This is the first root page.
+                """),
+                
+                TextFile(name: "SecondRoot.md", utf8Content: """
+                # Second Root
+                @Metadata {
+                   @TechnologyRoot
+                }
+                This is the second root page.
+                """),
+                
+                TextFile(name: "ThirdRoot.md", utf8Content: """
+                # Third Root
+                @Metadata {
+                   @TechnologyRoot
+                }
+                This is the third root page.
+                """),
+                
+                InfoPlist(displayName: "TestBundle", identifier: "com.test.example"),
+            ])
+        )
+        
+        // Verify that we emit warnings for multiple TechnologyRoot directives
+        let multipleRootsProblems = context.problems.filter { $0.diagnostic.identifier == "org.swift.docc.MultipleTechnologyRoots" }
+        XCTAssertEqual(multipleRootsProblems.count, 3, "Should emit warnings for all three TechnologyRoot directives")
+        
+        // Verify the warnings are associated with the correct files
+        let problemSources = multipleRootsProblems.compactMap { $0.diagnostic.source?.lastPathComponent }.sorted()
+        XCTAssertEqual(problemSources, ["FirstRoot.md", "SecondRoot.md", "ThirdRoot.md"])
+        
+        // Verify each warning has a solution to remove the TechnologyRoot directive
+        for problem in multipleRootsProblems {
+            XCTAssertEqual(problem.possibleSolutions.count, 1)
+            let solution = problem.possibleSolutions.first!
+            XCTAssertEqual(solution.summary, "Remove the 'TechnologyRoot' directive")
+            XCTAssertEqual(solution.replacements.count, 1)
+        }
+    }
+    
+    func testWarnsAboutMultipleMainModules() async throws {
+        // Create a bundle with multiple symbol graphs for different modules
+        let (_, context) = try await loadBundle(catalog:
+            Folder(name: "multiple-modules.docc", content: [
+                // First module symbol graph
+                TextFile(name: "ModuleA.symbols.json", utf8Content: """
+                {
+                  "metadata": {
+                    "formatVersion": {
+                      "major": 1,
+                      "minor": 0,
+                      "patch": 0
+                    },
+                    "generator": "unit-test"
+                  },
+                  "module": {
+                    "name": "ModuleA",
+                    "platform": {
+                      "architecture": "x86_64",
+                      "vendor": "apple",
+                      "operatingSystem": {
+                        "name": "macosx",
+                        "minimumVersion": {
+                          "major": 10,
+                          "minor": 15
+                        }
+                      },
+                      "environment": null
+                    }
+                  },
+                  "symbols": [
+                    {
+                      "identifier": {
+                        "precise": "ModuleA",
+                        "interfaceLanguage": "swift"
+                      },
+                      "names": {
+                        "title": "ModuleA",
+                        "navigator": null,
+                        "subHeading": null,
+                        "prose": null
+                      },
+                      "pathComponents": ["ModuleA"],
+                      "docComment": null,
+                      "accessLevel": "public",
+                      "kind": {
+                        "identifier": "module",
+                        "displayName": "Module"
+                      },
+                      "mixins": {}
+                    }
+                  ],
+                  "relationships": []
+                }
+                """),
+                
+                // Second module symbol graph
+                TextFile(name: "ModuleB.symbols.json", utf8Content: """
+                {
+                  "metadata": {
+                    "formatVersion": {
+                      "major": 1,
+                      "minor": 0,
+                      "patch": 0
+                    },
+                    "generator": "unit-test"
+                  },
+                  "module": {
+                    "name": "ModuleB",
+                    "platform": {
+                      "architecture": "x86_64",
+                      "vendor": "apple",
+                      "operatingSystem": {
+                        "name": "macosx",
+                        "minimumVersion": {
+                          "major": 10,
+                          "minor": 15
+                        }
+                      },
+                      "environment": null
+                    }
+                  },
+                  "symbols": [
+                    {
+                      "identifier": {
+                        "precise": "ModuleB",
+                        "interfaceLanguage": "swift"
+                      },
+                      "names": {
+                        "title": "ModuleB",
+                        "navigator": null,
+                        "subHeading": null,
+                        "prose": null
+                      },
+                      "pathComponents": ["ModuleB"],
+                      "docComment": null,
+                      "accessLevel": "public",
+                      "kind": {
+                        "identifier": "module",
+                        "displayName": "Module"
+                      },
+                      "mixins": {}
+                    }
+                  ],
+                  "relationships": []
+                }
+                """),
+                
+                InfoPlist(displayName: "TestBundle", identifier: "com.test.example"),
+            ])
+        )
+        
+        // Verify that we emit a warning for multiple main modules
+        let multipleModulesProblem = try XCTUnwrap(context.problems.first(where: { $0.diagnostic.identifier == "org.swift.docc.MultipleMainModules" }))
+        XCTAssertEqual(multipleModulesProblem.diagnostic.severity, .warning)
+        XCTAssertTrue(multipleModulesProblem.diagnostic.summary.contains("more than one main module"))
+        XCTAssertTrue(multipleModulesProblem.diagnostic.explanation?.contains("ModuleA, ModuleB") == true)
+        
+        // Verify the warning doesn't have a source location since it's about the overall input structure
+        XCTAssertNil(multipleModulesProblem.diagnostic.source)
+        XCTAssertNil(multipleModulesProblem.diagnostic.range)
+    }
 }