diff --git a/tmt/base/core.py b/tmt/base/core.py
index b08da78511..a59342a475 100644
--- a/tmt/base/core.py
+++ b/tmt/base/core.py
@@ -2923,8 +2923,8 @@ def __init__(
         self.policies = policies or []
         self.recipe_manager = RecipeManager(logger)
         self.recipe = None
-        if recipe_path is not None and self._tree is not None:
-            self.recipe = self.recipe_manager.load(self, recipe_path, self._tree.tree)
+        if recipe_path is not None:
+            self.recipe = self.recipe_manager.load(self, recipe_path)
 
     @property
     def run_workdir(self) -> Path:
diff --git a/tmt/recipe.py b/tmt/recipe.py
index 783101bc9f..5ff2adae54 100644
--- a/tmt/recipe.py
+++ b/tmt/recipe.py
@@ -1,6 +1,6 @@
 from typing import TYPE_CHECKING, Any, Callable, Optional, TypedDict, cast
 
-from fmf import Tree
+import fmf
 
 import tmt.utils
 from tmt.checks import Check, _RawCheck, normalize_test_checks
@@ -562,11 +562,12 @@ class RecipeManager(Common):
     def __init__(self, logger: Logger):
         super().__init__(logger=logger)
 
-    def load(self, run: 'Run', recipe_path: Path, fmf_tree: Tree) -> Recipe:
+    def load(self, run: 'Run', recipe_path: Path) -> Recipe:
         recipe = Recipe.from_spec(
-            cast(_RawRecipe, tmt.utils.yaml_to_dict(self.read(recipe_path))), self._logger
+            cast(_RawRecipe, tmt.utils.yaml_to_dict(self.read(recipe_path))),
+            self._logger,
         )
-        self._update_tree(recipe, fmf_tree)
+        self._update_tree(run, recipe)
         # TODO: We should have a way to set which steps are enabled
         # without modifying the CLI context directly.
         self._update_cli_context(recipe)
@@ -603,12 +604,18 @@ def tests(self, recipe: Recipe, plan_name: str) -> list[TestOrigin]:
         raise tmt.utils.GeneralError(f"Plan '{plan_name}' not found in the recipe.")
 
     @staticmethod
-    def _update_tree(recipe: Recipe, tree: Tree) -> None:
+    def _update_tree(run: 'Run', recipe: Recipe) -> None:
         """
-        Load the plans from the recipe and update the given fmf tree with their specifications.
+        Create a new fmf tree from the recipe's run and plan specifications.
         """
-        tree.children.clear()
-        tree.update({plan.name: plan.to_fmf_spec() for plan in recipe.plans})
+        from tmt.base.core import Tree
+
+        fmf_tree = fmf.Tree({plan.name: plan.to_fmf_spec() for plan in recipe.plans})
+        fmf_tree.root = recipe.run.root
+        for node in fmf_tree.climb():  # pyright: ignore[reportUnknownVariableType]
+            if isinstance(node, fmf.Tree):
+                node.root = recipe.run.root
+        run._tree = Tree(logger=run._logger, tree=fmf_tree)
 
     def _update_cli_context(self, recipe: Recipe) -> None:
         """