diff --git a/Sources/Commands/Error.swift b/Sources/Commands/Error.swift
index c6d6973f391..e6006d17054 100644
--- a/Sources/Commands/Error.swift
+++ b/Sources/Commands/Error.swift
@@ -23,6 +23,7 @@ public enum Error: ErrorProtocol {
     case invalidInstallation(String)
     case invalidSwiftExec(String)
     case buildYAMLNotFound(String)
+    case repositoryHasChanges(String)
 }
 
 extension Error: CustomStringConvertible {
@@ -38,6 +39,8 @@ extension Error: CustomStringConvertible {
             return "invalid SWIFT_EXEC value: \(value)"
         case .buildYAMLNotFound(let value):
             return "no build YAML found: \(value)"
+        case .repositoryHasChanges(let value):
+            return "repository has changes: \(value)"
         }
     }
 }
diff --git a/Sources/Commands/SwiftPackageTool.swift b/Sources/Commands/SwiftPackageTool.swift
index ad95045869a..e138ca2ecb3 100644
--- a/Sources/Commands/SwiftPackageTool.swift
+++ b/Sources/Commands/SwiftPackageTool.swift
@@ -179,6 +179,22 @@ public struct SwiftPackageTool {
                 try initPackage.writePackageStructure()
                             
             case .update:
+                // Attempt to ensure that none of the repositories are modified.
+                for item in walk(opts.path.Packages, recursively: false) {
+                    // Only look at repositories.
+                    guard Path.join(item, ".git").exists else { continue }
+
+                    // If there is a staged or unstaged diff, don't remove the
+                    // tree. This won't detect new untracked files, but it is
+                    // just a safety measure for now.
+                    let diffArgs = ["--no-ext-diff", "--quiet", "--exit-code"]
+                    do {
+                        _ = try Git.runPopen([Git.tool, "-C", item, "diff"] + diffArgs)
+                        _ = try Git.runPopen([Git.tool, "-C", item, "diff", "--cached"] + diffArgs)
+                    } catch {
+                        throw Error.repositoryHasChanges(item)
+                    }
+                }
                 try Utility.removeFileTree(opts.path.Packages)
                 fallthrough