diff --git a/pyproject.toml b/pyproject.toml
index c5ab0e5edcee..7fe1ef7843d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,6 +71,7 @@ pycryptodome = "^3.18.0"
 iterators = "^0.0.2"
 typer = { version = "^0.9.0", extras=["all"] }
 tomli = "^2.0.1"
+tomli-w = "^1.0.0"
 pathspec = "^0.12.1"
 # Optional dependencies (Simulation Engine)
 ray = { version = "==2.10.0", optional = true, python = ">=3.8,<3.12" }
diff --git a/src/py/flwr/cli/build.py b/src/py/flwr/cli/build.py
index 670b8bd64908..1f7f75d36184 100644
--- a/src/py/flwr/cli/build.py
+++ b/src/py/flwr/cli/build.py
@@ -20,6 +20,7 @@
 from typing import Optional
 
 import pathspec
+import tomli_w
 import typer
 from typing_extensions import Annotated
 
@@ -93,15 +94,28 @@ def build(
 
     allowed_extensions = {".py", ".toml", ".md"}
 
+    # Remove the 'federations' field from 'tool.flwr' if it exists
+    if (
+        "tool" in conf
+        and "flwr" in conf["tool"]
+        and "federations" in conf["tool"]["flwr"]
+    ):
+        del conf["tool"]["flwr"]["federations"]
+
+    toml_contents = tomli_w.dumps(conf)
+
     with zipfile.ZipFile(fab_filename, "w", zipfile.ZIP_DEFLATED) as fab_file:
+        fab_file.writestr("pyproject.toml", toml_contents)
+
+        # Continue with adding other files
         for root, _, files in os.walk(directory, topdown=True):
-            # Filter directories and files based on .gitignore
             files = [
                 f
                 for f in files
                 if not ignore_spec.match_file(Path(root) / f)
                 and f != fab_filename
                 and Path(f).suffix in allowed_extensions
+                and f != "pyproject.toml"  # Exclude the original pyproject.toml
             ]
 
             for file in files:
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.flowertune.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.flowertune.toml.tpl
index 5934a258564b..507b5d50b843 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.flowertune.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.flowertune.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets>=0.1.0,<1.0.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.hf.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.hf.toml.tpl
index 59f41f062af4..7a63e1ab5368 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.hf.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.hf.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets>=0.0.2,<1.0.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.jax.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.jax.toml.tpl
index 27f4b30ec3b8..297784a4d2d8 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.jax.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.jax.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = {text = "Apache License (2.0)"}
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "jax==0.4.26",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.mlx.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.mlx.toml.tpl
index 9c8905a0e8e5..fb55f6628cea 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.mlx.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.mlx.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets[vision]>=0.0.2,<1.0.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.numpy.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.numpy.toml.tpl
index 38bfa1888c4c..ae88472647dc 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.numpy.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.numpy.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "numpy>=1.21.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.pytorch.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.pytorch.toml.tpl
index 2fd366d8e350..2dd49a25fd90 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.pytorch.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.pytorch.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets[vision]>=0.0.2,<1.0.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.sklearn.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.sklearn.toml.tpl
index 143c3756858c..8458fa64ea2d 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.sklearn.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.sklearn.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets[vision]>=0.0.2,<1.0.0",
diff --git a/src/py/flwr/cli/new/templates/app/pyproject.tensorflow.toml.tpl b/src/py/flwr/cli/new/templates/app/pyproject.tensorflow.toml.tpl
index 964bef58c498..2bf0e7d5642c 100644
--- a/src/py/flwr/cli/new/templates/app/pyproject.tensorflow.toml.tpl
+++ b/src/py/flwr/cli/new/templates/app/pyproject.tensorflow.toml.tpl
@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "$package_name"
 version = "1.0.0"
 description = ""
-license = { text = "Apache License (2.0)" }
+license = "Apache-2.0"
 dependencies = [
     "flwr[simulation]>=1.9.0,<2.0",
     "flwr-datasets[vision]>=0.0.2,<1.0.0",