diff --git a/src/cli/init.rs b/src/cli/init.rs
index d3574554c..4185c2bf9 100644
--- a/src/cli/init.rs
+++ b/src/cli/init.rs
@@ -6,7 +6,7 @@ use std::{
 };
 
 use clap::{Parser, ValueEnum};
-use miette::IntoDiagnostic;
+use miette::{Context, IntoDiagnostic};
 use minijinja::{context, Environment};
 use pixi_config::{get_default_author, Config};
 use pixi_consts::consts;
@@ -15,6 +15,7 @@ use pixi_manifest::{
 };
 use pixi_utils::conda_environment_file::CondaEnvFile;
 use rattler_conda_types::{NamedChannelOrUrl, Platform};
+use tokio::fs::OpenOptions;
 use url::Url;
 
 use crate::Project;
@@ -349,6 +350,30 @@ pub async fn execute(args: Args) -> miette::Result<()> {
                 )
                 .unwrap();
             save_manifest_file(&pyproject_manifest_path, rv)?;
+            let src_dir = dir.join("src").join(default_name);
+            tokio::fs::create_dir_all(&src_dir)
+                .await
+                .into_diagnostic()
+                .wrap_err_with(|| format!("Could not create directory {}.", src_dir.display()))?;
+
+            let init_file = src_dir.join("__init__.py");
+            match OpenOptions::new()
+                .write(true)
+                .create_new(true)
+                .open(&init_file)
+                .await
+            {
+                Ok(_) => (),
+                Err(e) if e.kind() == ErrorKind::AlreadyExists => {
+                    // If the file already exists, do nothing
+                }
+                Err(e) => {
+                    return Err(e).into_diagnostic().wrap_err_with(|| {
+                        format!("Could not create file {}.", init_file.display())
+                    });
+                }
+            };
+
         // Create a 'pixi.toml' manifest
         } else {
             // Check if the 'pixi.toml' file doesn't already exist. We don't want to
diff --git a/tests/integration/test_main_cli.py b/tests/integration/test_main_cli.py
index 9684832c0..4364f4ebd 100644
--- a/tests/integration/test_main_cli.py
+++ b/tests/integration/test_main_cli.py
@@ -234,3 +234,11 @@ def test_simple_project_setup(tmp_path: Path) -> None:
         ExitCode.SUCCESS,
         stderr_contains=["osx-arm64", "test", "Removed"],
     )
+
+
+def test_pixi_init_pyproject(tmp_path: Path) -> None:
+    manifest_path = tmp_path / "pyproject.toml"
+    # Create a new project
+    verify_cli_command(f"pixi init {tmp_path} --pyproject-toml", ExitCode.SUCCESS)
+    # Verify that install works
+    verify_cli_command(f"pixi install --manifest-path {manifest_path}", ExitCode.SUCCESS)