diff --git a/CHANGELOG.md b/CHANGELOG.md
index da1dd17..6be48c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@
   - `upsert: <pattern>` + `with: <line>` — replaces if pattern matches, otherwise appends
 - MFA required to publish this gem
 
+### ⚠️ Behavior changes
+
+- `.worktree.yml` in the linked worktree now drives **all** setup steps, not just the tail end. Previously `copy:` and `link:` always came from the main worktree's config while the rest came from the linked one if present — split that produced surprising results. Now: linked config wins entirely if present; main is the fallback. No effect unless you have a linked `.worktree.yml` whose `copy:`/`link:` differs from main's.
+
 ## 0.6.0
 
 ### ✨ Features
diff --git a/README.md b/README.md
index f5286a0..eba066e 100644
--- a/README.md
+++ b/README.md
@@ -103,6 +103,17 @@ setup: mise exec -- bin/setup
 
 `bonchi create` auto-runs setup when `.worktree.yml` exists. Skip with `--no-setup`.
 
+If `.worktree.yml` exists in the linked worktree, it takes precedence over the main worktree's — useful for trying out config changes in a single worktree without touching main, or for committing a per-branch config. The main worktree's config is the fallback when no local config is present.
+
+To pin every new worktree to its own copy of the config (full isolation, no propagation of later edits in main), add it to `copy:`:
+
+```yaml
+copy:
+  - .worktree.yml
+```
+
+Default is to leave it out, so edits to main's `.worktree.yml` automatically apply to every subsequent `bonchi setup` run.
+
 ### Edit
 
 Use `edit` to modify files during setup. Three actions are available; entries run in order, so you can interleave them. Env vars (`$VAR`) are expanded in replacement values.
diff --git a/lib/bonchi/setup.rb b/lib/bonchi/setup.rb
index 0ed3455..d190ea4 100644
--- a/lib/bonchi/setup.rb
+++ b/lib/bonchi/setup.rb
@@ -21,8 +21,13 @@ def run(args = [], upto: nil)
         abort "#{color(:red)}Error:#{reset} already in the main worktree"
       end
 
-      config = Config.from_main_worktree
-      abort "#{color(:red)}Error:#{reset} .worktree.yml not found in main worktree" unless config
+      config = Config.from_worktree(@worktree)
+      if config
+        puts "Using .worktree.yml from linked worktree"
+      else
+        config = Config.from_main_worktree
+        abort "#{color(:red)}Error:#{reset} .worktree.yml not found in main worktree" unless config
+      end
 
       last_step = upto || STEPS.last
       run_steps = STEPS[0..STEPS.index(last_step)]
@@ -37,14 +42,6 @@ def run(args = [], upto: nil)
 
       copy_files(config.copy) if run_steps.include?("copy")
       link_files(config.link) if run_steps.include?("link")
-
-      # Prefer linked worktree's .worktree.yml if it was copied or already exists
-      linked_config = Config.from_worktree(@worktree)
-      if linked_config
-        puts "Using .worktree.yml from linked worktree"
-        config = linked_config
-      end
-
       allocate_ports(config.ports) if run_steps.include?("ports") && config.ports.any?
       replace_in_files(config.replace) if run_steps.include?("replace") && config.replace.any?
       run_pre_setup(config.pre_setup) if run_steps.include?("pre_setup")
diff --git a/test/test_setup.rb b/test/test_setup.rb
index 92f8f47..990316d 100644
--- a/test/test_setup.rb
+++ b/test/test_setup.rb
@@ -142,3 +142,84 @@ def test_missing_file_aborts
     end
   end
 end
+
+class TestSetupConfigSource < Minitest::Test
+  def setup
+    @tmpdir = Dir.mktmpdir
+    @main = File.join(@tmpdir, "main")
+    @linked = File.join(@tmpdir, "linked")
+    FileUtils.mkdir_p(@main)
+    FileUtils.mkdir_p(@linked)
+    @setup = Bonchi::Setup.allocate
+    @setup.instance_variable_set(:@worktree, @linked)
+    @setup.instance_variable_set(:@main_worktree, @main)
+    ENV["WORKTREE_ROOT"] = @tmpdir
+  end
+
+  def teardown
+    FileUtils.remove_entry(@tmpdir)
+    %w[WORKTREE_ROOT WORKTREE_BRANCH WORKTREE_BRANCH_SLUG WORKTREE_MAIN WORKTREE_LINKED].each { |k| ENV.delete(k) }
+  end
+
+  def write(dir, file, content)
+    path = File.join(dir, file)
+    FileUtils.mkdir_p(File.dirname(path))
+    File.write(path, content)
+  end
+
+  def silenced
+    out = $stdout
+    $stdout = StringIO.new
+    yield
+  ensure
+    $stdout = out
+  end
+
+  def run_setup(upto:)
+    Bonchi::Git.stub(:main_worktree, @main) do
+      Bonchi::Git.stub(:current_branch, "feat/x") do
+        silenced { @setup.run([], upto: upto) }
+      end
+    end
+  end
+
+  def test_linked_copy_takes_precedence_over_main
+    write(@main, "from-main.txt", "main\n")
+    write(@main, "from-linked.txt", "linked\n")
+    write(@main, ".worktree.yml", "copy:\n  - from-main.txt\n")
+    write(@linked, ".worktree.yml", "copy:\n  - from-linked.txt\n")
+
+    run_setup(upto: "copy")
+
+    refute File.exist?(File.join(@linked, "from-main.txt")), "main's copy entry should be ignored when linked config exists"
+    assert_equal "linked\n", File.read(File.join(@linked, "from-linked.txt"))
+  end
+
+  def test_linked_link_takes_precedence_over_main
+    write(@main, "from-main", "m\n")
+    write(@main, "from-linked", "l\n")
+    write(@main, ".worktree.yml", "link:\n  - from-main\n")
+    write(@linked, ".worktree.yml", "link:\n  - from-linked\n")
+
+    run_setup(upto: "link")
+
+    refute File.exist?(File.join(@linked, "from-main"))
+    assert File.symlink?(File.join(@linked, "from-linked"))
+    assert_equal File.join(@main, "from-linked"), File.readlink(File.join(@linked, "from-linked"))
+  end
+
+  def test_falls_back_to_main_when_linked_has_no_config
+    write(@main, "tool.toml", "m\n")
+    write(@main, ".worktree.yml", "copy:\n  - tool.toml\n")
+
+    run_setup(upto: "copy")
+
+    assert_equal "m\n", File.read(File.join(@linked, "tool.toml"))
+  end
+
+  def test_aborts_when_neither_worktree_has_config
+    assert_raises(SystemExit) do
+      run_setup(upto: "copy")
+    end
+  end
+end