diff --git a/src/cli.rs b/src/cli.rs
index 7acc241..9068da6 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -10,7 +10,7 @@ use env_logger::fmt::WriteStyle;
 use crate::{
     command::{self, apply::DeployOpts},
     error::ColmenaResult,
-    nix::{Hive, HivePath},
+    nix::{hive::EvaluationMethod, Hive, HivePath},
 };
 
 /// Base URL of the manual, without the trailing slash.
@@ -137,6 +137,21 @@ This only works when building locally.
         value_names = ["NAME", "VALUE"],
     )]
     nix_option: Vec<String>,
+    #[arg(
+        long,
+        default_value_t,
+        help = "Use direct flake evaluation (experimental)",
+        long_help = r#"If enabled, flakes will be evaluated using `nix eval`. This requires the flake to depend on Colmena as an input and expose a compatible `colmenaHive` output:
+
+  outputs = { self, colmena, ... }: {
+    colmenaHive = colmena.lib.makeHive self.outputs.colmena;
+    colmena = ...;
+  };
+
+This is an experimental feature."#,
+        global = true
+    )]
+    experimental_flake_eval: bool,
     #[arg(
         long,
         value_name = "WHEN",
@@ -262,6 +277,11 @@ async fn get_hive(opts: &Opts) -> ColmenaResult<Hive> {
         hive.set_impure(true);
     }
 
+    if opts.experimental_flake_eval {
+        log::warn!("Using direct flake evaluation (experimental)");
+        hive.set_evaluation_method(EvaluationMethod::DirectFlakeEval);
+    }
+
     for chunks in opts.nix_option.chunks_exact(2) {
         let [name, value] = chunks else {
             unreachable!()
diff --git a/src/nix/hive/mod.rs b/src/nix/hive/mod.rs
index f9d9227..2faa88e 100644
--- a/src/nix/hive/mod.rs
+++ b/src/nix/hive/mod.rs
@@ -8,6 +8,7 @@ use std::convert::AsRef;
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
 
+use const_format::formatcp;
 use tokio::process::Command;
 use tokio::sync::OnceCell;
 use validator::Validate;
@@ -22,6 +23,21 @@ use crate::job::JobHandle;
 use crate::util::{CommandExecution, CommandExt};
 use assets::Assets;
 
+/// The version of the Hive schema we are compatible with.
+///
+/// Currently we are tied to one specific version.
+const HIVE_SCHEMA: &str = "v0.20241006";
+
+/// The snippet to be used for `nix eval --apply`.
+const FLAKE_APPLY_SNIPPET: &str = formatcp!(
+    r#"with builtins; hive: assert (hive.__schema == "{}" || throw ''
+    The colmenaHive output (schema ${{hive.__schema}}) isn't compatible with this version of Colmena.
+
+    Hint: Use the same version of Colmena as in the Flake input.
+''); "#,
+    HIVE_SCHEMA
+);
+
 #[derive(Debug, Clone)]
 pub enum HivePath {
     /// A Nix Flake.
@@ -63,11 +79,33 @@ impl FromStr for HivePath {
     }
 }
 
+#[derive(Debug, Clone, Copy, PartialEq)]
+pub enum EvaluationMethod {
+    /// Use nix-instantiate and specify the entire Nix expression.
+    ///
+    /// This is the default method.
+    ///
+    /// For flakes, we use `builtins.getFlakes`. Pure evaluation no longer works
+    /// with this method in Nix 2.21+.
+    NixInstantiate,
+
+    /// Use `nix eval --apply` on top of a flake.
+    ///
+    /// This can be activated with --experimental-flake-eval.
+    ///
+    /// In this method, we can no longer pull in our bundled assets and
+    /// the flake must expose a compatible `colmenaHive` output.
+    DirectFlakeEval,
+}
+
 #[derive(Debug)]
 pub struct Hive {
     /// Path to the hive.
     path: HivePath,
 
+    /// Method to evaluate the hive with.
+    evaluation_method: EvaluationMethod,
+
     /// Path to the context directory.
     ///
     /// Normally this is directory containing the "hive.nix"
@@ -134,6 +172,7 @@ impl Hive {
 
         Ok(Self {
             path,
+            evaluation_method: EvaluationMethod::NixInstantiate,
             context_dir,
             assets,
             show_trace: false,
@@ -158,6 +197,14 @@ impl Hive {
             .await
     }
 
+    pub fn set_evaluation_method(&mut self, method: EvaluationMethod) {
+        if !self.is_flake() && method == EvaluationMethod::DirectFlakeEval {
+            return;
+        }
+
+        self.evaluation_method = method;
+    }
+
     pub fn set_show_trace(&mut self, value: bool) {
         self.show_trace = value;
     }
@@ -421,7 +468,10 @@ impl Hive {
 
     /// Returns the base expression from which the evaluated Hive can be used.
     fn get_base_expression(&self) -> String {
-        self.assets.get_base_expression()
+        match self.evaluation_method {
+            EvaluationMethod::NixInstantiate => self.assets.get_base_expression(),
+            EvaluationMethod::DirectFlakeEval => FLAKE_APPLY_SNIPPET.to_string(),
+        }
     }
 
     /// Returns whether this Hive is a flake.
@@ -444,6 +494,11 @@ impl<'hive> NixInstantiate<'hive> {
     }
 
     fn instantiate(&self) -> Command {
+        // TODO: Better error handling
+        if self.hive.evaluation_method == EvaluationMethod::DirectFlakeEval {
+            panic!("Instantiation is not supported with DirectFlakeEval");
+        }
+
         let mut command = Command::new("nix-instantiate");
 
         if self.hive.is_flake() {
@@ -462,17 +517,48 @@ impl<'hive> NixInstantiate<'hive> {
     }
 
     fn eval(self) -> Command {
-        let mut command = self.instantiate();
         let flags = self.hive.nix_flags();
-        command
-            .arg("--eval")
-            .arg("--json")
-            .arg("--strict")
-            // Ensures the derivations are instantiated
-            // Required for system profile evaluation and IFD
-            .arg("--read-write-mode")
-            .args(flags.to_args());
-        command
+
+        match self.hive.evaluation_method {
+            EvaluationMethod::NixInstantiate => {
+                let mut command = self.instantiate();
+
+                command
+                    .arg("--eval")
+                    .arg("--json")
+                    .arg("--strict")
+                    // Ensures the derivations are instantiated
+                    // Required for system profile evaluation and IFD
+                    .arg("--read-write-mode")
+                    .args(flags.to_args());
+
+                command
+            }
+            EvaluationMethod::DirectFlakeEval => {
+                let mut command = Command::new("nix");
+                let flake = if let HivePath::Flake(flake) = self.hive.path() {
+                    flake
+                } else {
+                    panic!("The DirectFlakeEval evaluation method only support flakes");
+                };
+
+                let hive_installable = format!("{}#colmenaHive", flake.uri());
+
+                let mut full_expression = self.hive.get_base_expression();
+                full_expression += &self.expression;
+
+                command
+                    .arg("eval") // nix eval
+                    .args(["--extra-experimental-features", "flakes nix-command"])
+                    .arg(hive_installable)
+                    .arg("--json")
+                    .arg("--apply")
+                    .arg(&full_expression)
+                    .args(flags.to_args());
+
+                command
+            }
+        }
     }
 
     async fn instantiate_with_builders(self) -> ColmenaResult<Command> {