diff --git a/src/nix/flake.cc b/src/nix/flake.cc
index 8370b8dcf..c66b24e5c 100644
--- a/src/nix/flake.cc
+++ b/src/nix/flake.cc
@@ -740,7 +740,8 @@ struct CmdFlakeInitCommon : virtual Args, EvalCommand
                 "If you've set '%s' to a string, try using a path instead.",
                 templateDir, templateDirAttr->getAttrPathStr());
 
-        std::vector<Path> files;
+        std::vector<Path> changedFiles;
+        std::vector<Path> conflictedFiles;
 
         std::function<void(const Path & from, const Path & to)> copyDir;
         copyDir = [&](const Path & from, const Path & to)
@@ -757,31 +758,41 @@ struct CmdFlakeInitCommon : virtual Args, EvalCommand
                     auto contents = readFile(from2);
                     if (pathExists(to2)) {
                         auto contents2 = readFile(to2);
-                        if (contents != contents2)
-                            throw Error("refusing to overwrite existing file '%s'", to2);
+                        if (contents != contents2) {
+                            printError("refusing to overwrite existing file '%s'\n please merge it manually with '%s'", to2, from2);
+                            conflictedFiles.push_back(to2);
+                        } else {
+                            notice("skipping identical file: %s", from2);
+                        }
+                        continue;
                     } else
                         writeFile(to2, contents);
                 }
                 else if (S_ISLNK(st.st_mode)) {
                     auto target = readLink(from2);
                     if (pathExists(to2)) {
-                        if (readLink(to2) != target)
-                            throw Error("refusing to overwrite existing symlink '%s'", to2);
+                        if (readLink(to2) != target) {
+                            printError("refusing to overwrite existing file '%s'\n please merge it manually with '%s'", to2, from2);
+                            conflictedFiles.push_back(to2);
+                        } else {
+                            notice("skipping identical file: %s", from2);
+                        }
+                        continue;
                     } else
                           createSymlink(target, to2);
                 }
                 else
                     throw Error("file '%s' has unsupported type", from2);
-                files.push_back(to2);
+                changedFiles.push_back(to2);
                 notice("wrote: %s", to2);
             }
         };
 
         copyDir(templateDir, flakeDir);
 
-        if (pathExists(flakeDir + "/.git")) {
+        if (!changedFiles.empty() && pathExists(flakeDir + "/.git")) {
             Strings args = { "-C", flakeDir, "add", "--intent-to-add", "--force", "--" };
-            for (auto & s : files) args.push_back(s);
+            for (auto & s : changedFiles) args.push_back(s);
             runProgram("git", true, args);
         }
         auto welcomeText = cursor->maybeGetAttr("welcomeText");
@@ -789,6 +800,9 @@ struct CmdFlakeInitCommon : virtual Args, EvalCommand
             notice("\n");
             notice(renderMarkdownToTerminal(welcomeText->getString()));
         }
+
+        if (!conflictedFiles.empty())
+            throw Error("Encountered %d conflicts - see above", conflictedFiles.size());
     }
 };
 
diff --git a/tests/flakes.sh b/tests/flakes.sh
index 36bffcf3b..35cf4d8e7 100644
--- a/tests/flakes.sh
+++ b/tests/flakes.sh
@@ -408,8 +408,10 @@ cat > $templatesDir/trivial/flake.nix <<EOF
   };
 }
 EOF
+echo a > $templatesDir/trivial/a
+echo b > $templatesDir/trivial/b
 
-git -C $templatesDir add flake.nix trivial/flake.nix
+git -C $templatesDir add flake.nix trivial/
 git -C $templatesDir commit -m 'Initial'
 
 nix flake check templates
@@ -424,6 +426,18 @@ nix flake show $flake7Dir
 nix flake show $flake7Dir --json | jq
 git -C $flake7Dir commit -a -m 'Initial'
 
+# Test 'nix flake init' with benign conflicts
+rm -rf $flake7Dir && mkdir $flake7Dir && git -C $flake7Dir init
+echo a > $flake7Dir/a
+(cd $flake7Dir && nix flake init) # check idempotence
+
+# Test 'nix flake init' with conflicts
+rm -rf $flake7Dir && mkdir $flake7Dir && git -C $flake7Dir init
+echo b > $flake7Dir/a
+pushd $flake7Dir
+(! nix flake init) |& grep "refusing to overwrite existing file '$flake7Dir/a'"
+popd
+
 # Test 'nix flake new'.
 rm -rf $flake6Dir
 nix flake new -t templates#trivial $flake6Dir