diff --git a/crates/puffin-installer/src/plan.rs b/crates/puffin-installer/src/plan.rs
index 0c80ca0eb..4f9745ba9 100644
--- a/crates/puffin-installer/src/plan.rs
+++ b/crates/puffin-installer/src/plan.rs
@@ -142,9 +142,19 @@ impl InstallPlan {
         }
 
         // Remove any unnecessary packages.
-        for (_package, dist_info) in site_packages {
-            debug!("Unnecessary package: {dist_info}");
-            extraneous.push(dist_info);
+        if !site_packages.is_empty() {
+            // If Puffin created the virtual environment, then remove all packages, regardless of
+            // whether they're considered "seed" packages.
+            let seed_packages = !venv.cfg().is_ok_and(|cfg| cfg.is_gourgeist());
+            for (package, dist_info) in site_packages {
+                if seed_packages && matches!(package.as_ref(), "pip" | "setuptools" | "wheel") {
+                    debug!("Preserving seed package: {dist_info}");
+                    continue;
+                }
+
+                debug!("Unnecessary package: {dist_info}");
+                extraneous.push(dist_info);
+            }
         }
 
         Ok(InstallPlan {
diff --git a/crates/puffin-installer/src/site_packages.rs b/crates/puffin-installer/src/site_packages.rs
index 9e845d9a5..346b2ef40 100644
--- a/crates/puffin-installer/src/site_packages.rs
+++ b/crates/puffin-installer/src/site_packages.rs
@@ -45,6 +45,16 @@ impl SitePackages {
     pub fn remove(&mut self, name: &PackageName) -> Option<InstalledDist> {
         self.0.remove(name)
     }
+
+    /// Returns `true` if there are no installed packages.
+    pub fn is_empty(&self) -> bool {
+        self.0.is_empty()
+    }
+
+    /// Returns the number of installed packages.
+    pub fn len(&self) -> usize {
+        self.0.len()
+    }
 }
 
 impl IntoIterator for SitePackages {
diff --git a/crates/puffin-interpreter/src/cfg.rs b/crates/puffin-interpreter/src/cfg.rs
new file mode 100644
index 000000000..68920791a
--- /dev/null
+++ b/crates/puffin-interpreter/src/cfg.rs
@@ -0,0 +1,60 @@
+use std::path::Path;
+
+use fs_err as fs;
+use thiserror::Error;
+
+#[derive(Debug, Clone)]
+pub struct Configuration {
+    /// The version of the `virtualenv` package used to create the virtual environment, if any.
+    pub(crate) virtualenv: bool,
+    /// The version of the `gourgeist` package used to create the virtual environment, if any.
+    pub(crate) gourgeist: bool,
+}
+
+impl Configuration {
+    /// Parse a `pyvenv.cfg` file into a [`Configuration`].
+    pub fn parse(cfg: impl AsRef<Path>) -> Result<Self, Error> {
+        let mut virtualenv = false;
+        let mut gourgeist = false;
+
+        // Per https://snarky.ca/how-virtual-environments-work/, the `pyvenv.cfg` file is not a
+        // valid INI file, and is instead expected to be parsed by partitioning each line on the
+        // first equals sign.
+        let content = fs::read_to_string(&cfg)?;
+        for line in content.lines() {
+            let Some((key, _value)) = line.split_once('=') else {
+                continue;
+            };
+            match key.trim() {
+                "virtualenv" => {
+                    virtualenv = true;
+                }
+                "gourgeist" => {
+                    gourgeist = true;
+                }
+                _ => {}
+            }
+        }
+
+        Ok(Self {
+            virtualenv,
+            gourgeist,
+        })
+    }
+
+    /// Returns true if the virtual environment was created with the `virtualenv` package.
+    pub fn is_virtualenv(&self) -> bool {
+        self.virtualenv
+    }
+
+    /// Returns true if the virtual environment was created with the `gourgeist` package.
+    pub fn is_gourgeist(&self) -> bool {
+        self.gourgeist
+    }
+}
+
+#[derive(Debug, Error)]
+pub enum Error {
+    #[error(transparent)]
+    Io(#[from] std::io::Error),
+}
diff --git a/crates/puffin-interpreter/src/lib.rs b/crates/puffin-interpreter/src/lib.rs
index 80875b9f7..524a05fdf 100644
--- a/crates/puffin-interpreter/src/lib.rs
+++ b/crates/puffin-interpreter/src/lib.rs
@@ -7,6 +7,7 @@ use thiserror::Error;
 pub use crate::interpreter::Interpreter;
 pub use crate::virtual_env::Virtualenv;
 
+mod cfg;
 mod interpreter;
 mod python_platform;
 mod virtual_env;
@@ -39,4 +40,6 @@ pub enum Error {
     },
     #[error("Failed to write to cache")]
     Serde(#[from] serde_json::Error),
+    #[error("Failed to parse pyvenv.cfg")]
+    Cfg(#[from] cfg::Error),
 }
diff --git a/crates/puffin-interpreter/src/virtual_env.rs b/crates/puffin-interpreter/src/virtual_env.rs
index 7853980b1..696080f98 100644
--- a/crates/puffin-interpreter/src/virtual_env.rs
+++ b/crates/puffin-interpreter/src/virtual_env.rs
@@ -6,6 +6,7 @@ use tracing::debug;
 use platform_host::Platform;
 use puffin_cache::Cache;
 
+use crate::cfg::Configuration;
 use crate::python_platform::PythonPlatform;
 use crate::{Error, Interpreter};
 
@@ -66,10 +67,17 @@ impl Virtualenv {
         &self.root
     }
 
+    /// Return the [`Interpreter`] for this virtual environment.
     pub fn interpreter(&self) -> &Interpreter {
         &self.interpreter
     }
 
+    /// Return the [`Configuration`] for this virtual environment, as extracted from the
+    /// `pyvenv.cfg` file.
+    pub fn cfg(&self) -> Result<Configuration, Error> {
+        Ok(Configuration::parse(self.root.join("pyvenv.cfg"))?)
+    }
+
     /// Returns the path to the `site-packages` directory inside a virtual environment.
     pub fn site_packages(&self) -> PathBuf {
         self.interpreter