diff --git a/crates/capsule-cli/Cargo.lock b/crates/capsule-cli/Cargo.lock
index 81b1c33..c31895e 100644
--- a/crates/capsule-cli/Cargo.lock
+++ b/crates/capsule-cli/Cargo.lock
@@ -115,6 +115,18 @@ version = "1.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c3d036a3c4ab069c7b410a2ce876bd74808d2d0888a82667669f8e783a898bf1"
 
+[[package]]
+name = "arrayref"
+version = "0.3.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "76a2e8124351fda1ef8aaaa3bbd7ebbcb486bbcd4225aca0aa0d84bb2db8fecb"
+
+[[package]]
+name = "arrayvec"
+version = "0.7.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7c02d123df017efcdfbd739ef81735b36c5ba83ec3c59c80a9d7ecc718f92e50"
+
 [[package]]
 name = "ast_node"
 version = "5.0.0"
@@ -176,6 +188,20 @@ version = "2.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "812e12b5285cc515a9c72a5c1d3b6d46a19dac5acfef5265968c166106e31dd3"
 
+[[package]]
+name = "blake3"
+version = "1.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2468ef7d57b3fb7e16b576e8377cdbde2320c60e1491e961d11da40fc4f02a2d"
+dependencies = [
+ "arrayref",
+ "arrayvec",
+ "cc",
+ "cfg-if",
+ "constant_time_eq",
+ "cpufeatures",
+]
+
 [[package]]
 name = "block-buffer"
 version = "0.10.4"
@@ -299,6 +325,7 @@ name = "capsule-core"
 version = "0.4.0"
 dependencies = [
  "anyhow",
+ "blake3",
  "chrono",
  "colored",
  "humantime",
@@ -444,6 +471,12 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
+[[package]]
+name = "constant_time_eq"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3d52eff69cd5e647efe296129160853a42795992097e8af39800e1060caeea9b"
+
 [[package]]
 name = "core-foundation-sys"
 version = "0.8.7"
diff --git a/crates/capsule-core/Cargo.lock b/crates/capsule-core/Cargo.lock
index 21b14d6..4fa3355 100644
--- a/crates/capsule-core/Cargo.lock
+++ b/crates/capsule-core/Cargo.lock
@@ -74,6 +74,18 @@ version = "1.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c3d036a3c4ab069c7b410a2ce876bd74808d2d0888a82667669f8e783a898bf1"
 
+[[package]]
+name = "arrayref"
+version = "0.3.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "76a2e8124351fda1ef8aaaa3bbd7ebbcb486bbcd4225aca0aa0d84bb2db8fecb"
+
+[[package]]
+name = "arrayvec"
+version = "0.7.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7c02d123df017efcdfbd739ef81735b36c5ba83ec3c59c80a9d7ecc718f92e50"
+
 [[package]]
 name = "ast_node"
 version = "5.0.0"
@@ -156,6 +168,20 @@ version = "2.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "812e12b5285cc515a9c72a5c1d3b6d46a19dac5acfef5265968c166106e31dd3"
 
+[[package]]
+name = "blake3"
+version = "1.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2468ef7d57b3fb7e16b576e8377cdbde2320c60e1491e961d11da40fc4f02a2d"
+dependencies = [
+ "arrayref",
+ "arrayvec",
+ "cc",
+ "cfg-if",
+ "constant_time_eq",
+ "cpufeatures",
+]
+
 [[package]]
 name = "block-buffer"
 version = "0.10.4"
@@ -279,6 +305,7 @@ name = "capsule-core"
 version = "0.4.0"
 dependencies = [
  "anyhow",
+ "blake3",
  "chrono",
  "colored",
  "humantime",
@@ -378,6 +405,12 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
+[[package]]
+name = "constant_time_eq"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3d52eff69cd5e647efe296129160853a42795992097e8af39800e1060caeea9b"
+
 [[package]]
 name = "core-foundation-sys"
 version = "0.8.7"
diff --git a/crates/capsule-core/Cargo.toml b/crates/capsule-core/Cargo.toml
index f2450a5..288d9ff 100644
--- a/crates/capsule-core/Cargo.toml
+++ b/crates/capsule-core/Cargo.toml
@@ -28,6 +28,7 @@ indicatif = "0.17"
 chrono = "0.4"
 colored = "2.1"
 toml = "0.9.11"
+blake3 = "1"
 
 rustpython-parser = "0.4"
 swc_ecma_parser = "33.0"
diff --git a/crates/capsule-core/src/config/fingerprint.rs b/crates/capsule-core/src/config/fingerprint.rs
new file mode 100644
index 0000000..59a9daf
--- /dev/null
+++ b/crates/capsule-core/src/config/fingerprint.rs
@@ -0,0 +1,218 @@
+use std::collections::BTreeMap;
+use std::fs;
+use std::path::{Path, PathBuf};
+
+use serde::{Deserialize, Serialize};
+
+#[derive(Debug, Serialize, Deserialize, Default)]
+pub struct SourceFingerprint {
+    pub files: BTreeMap<String, String>,
+}
+
+impl SourceFingerprint {
+    const MANIFEST_FILENAME: &'static str = ".capsule_fingerprint.json";
+
+    pub fn load(cache_dir: &Path) -> Self {
+        let fingerprint_path = cache_dir.join(Self::MANIFEST_FILENAME);
+
+        if fingerprint_path.exists()
+            && let Ok(content) = fs::read_to_string(&fingerprint_path)
+            && let Ok(fingerprint) = serde_json::from_str(&content)
+        {
+            return fingerprint;
+        }
+
+        Self::default()
+    }
+
+    pub fn save(&self, cache_dir: &Path) -> std::io::Result<()> {
+        let fingerprint_path = cache_dir.join(Self::MANIFEST_FILENAME);
+        let content = serde_json::to_string_pretty(self)?;
+        fs::write(fingerprint_path, content)
+    }
+
+    pub fn hash_file(path: &Path) -> Option<String> {
+        let contents = fs::read(path).ok()?;
+        Some(blake3::hash(&contents).to_hex().to_string())
+    }
+
+    pub fn collect_source_files(
+        base_dir: &Path,
+        extensions: &[&str],
+        ignored_dirs: &[&str],
+    ) -> Vec<PathBuf> {
+        let mut files = Vec::new();
+        Self::collect_files_recursive(base_dir, extensions, ignored_dirs, &mut files);
+        files
+    }
+
+    fn collect_files_recursive(
+        dir: &Path,
+        extensions: &[&str],
+        ignored_dirs: &[&str],
+        files: &mut Vec<PathBuf>,
+    ) {
+        let Ok(entries) = fs::read_dir(dir) else {
+            return;
+        };
+
+        for entry in entries.flatten() {
+            let path = entry.path();
+
+            if path.is_dir() {
+                let dir_name = path.file_name().and_then(|n| n.to_str()).unwrap_or("");
+
+                if dir_name.starts_with('.') || ignored_dirs.contains(&dir_name) {
+                    continue;
+                }
+
+                Self::collect_files_recursive(&path, extensions, ignored_dirs, files);
+            } else if let Some(ext) = path.extension().and_then(|e| e.to_str())
+                && extensions.contains(&ext)
+            {
+                files.push(path);
+            }
+        }
+    }
+
+    pub fn build(base_dir: &Path, extensions: &[&str], ignored_dirs: &[&str]) -> Self {
+        let files = Self::collect_source_files(base_dir, extensions, ignored_dirs);
+        let mut fingerprint = Self::default();
+
+        for file_path in files {
+            if let Some(hash) = Self::hash_file(&file_path) {
+                let relative = file_path
+                    .strip_prefix(base_dir)
+                    .unwrap_or(&file_path)
+                    .to_string_lossy()
+                    .to_string();
+                fingerprint.files.insert(relative, hash);
+            }
+        }
+
+        fingerprint
+    }
+
+    pub fn has_changes(&self, other: &SourceFingerprint) -> bool {
+        if self.files.len() != other.files.len() {
+            return true;
+        }
+
+        for (path, hash) in &self.files {
+            match other.files.get(path) {
+                Some(other_hash) if hash == other_hash => continue,
+                _ => return true,
+            }
+        }
+
+        false
+    }
+
+    pub fn needs_rebuild(
+        cache_dir: &Path,
+        source_dir: &Path,
+        output_path: &Path,
+        extensions: &[&str],
+        ignored_dirs: &[&str],
+    ) -> bool {
+        if !output_path.exists() {
+            return true;
+        }
+        let previous = Self::load(cache_dir);
+
+        let current = Self::build(source_dir, extensions, ignored_dirs);
+
+        current.has_changes(&previous)
+    }
+
+    pub fn update_after_build(
+        cache_dir: &Path,
+        source_dir: &Path,
+        extensions: &[&str],
+        ignored_dirs: &[&str],
+    ) -> std::io::Result<()> {
+        let fingerprint = Self::build(source_dir, extensions, ignored_dirs);
+        fingerprint.save(cache_dir)
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_hash_consistency() {
+        let hash1 = blake3::hash(b"hello world").to_hex().to_string();
+        let hash2 = blake3::hash(b"hello world").to_hex().to_string();
+        assert_eq!(hash1, hash2);
+
+        let hash3 = blake3::hash(b"goodbye world").to_hex().to_string();
+        assert_ne!(hash1, hash3);
+    }
+
+    #[test]
+    fn test_fingerprint_no_changes() {
+        let mut fingerprint1 = SourceFingerprint::default();
+        fingerprint1
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+
+        let mut fingerprint2 = SourceFingerprint::default();
+        fingerprint2
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+
+        assert!(!fingerprint1.has_changes(&fingerprint2));
+    }
+
+    #[test]
+    fn test_fingerprint_content_changed() {
+        let mut fingerprint1 = SourceFingerprint::default();
+        fingerprint1
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+
+        let mut fingerprint2 = SourceFingerprint::default();
+        fingerprint2
+            .files
+            .insert("main.py".to_string(), "xyz789".to_string());
+
+        assert!(fingerprint1.has_changes(&fingerprint2));
+    }
+
+    #[test]
+    fn test_fingerprint_file_added() {
+        let mut fingerprint1 = SourceFingerprint::default();
+        fingerprint1
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+
+        let mut fingerprint2 = SourceFingerprint::default();
+        fingerprint2
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+        fingerprint2
+            .files
+            .insert("helper.py".to_string(), "def456".to_string());
+
+        assert!(fingerprint1.has_changes(&fingerprint2));
+    }
+
+    #[test]
+    fn test_fingerprint_file_deleted() {
+        let mut fingerprint1 = SourceFingerprint::default();
+        fingerprint1
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+        fingerprint1
+            .files
+            .insert("helper.py".to_string(), "def456".to_string());
+
+        let mut fingerprint2 = SourceFingerprint::default();
+        fingerprint2
+            .files
+            .insert("main.py".to_string(), "abc123".to_string());
+
+        assert!(fingerprint1.has_changes(&fingerprint2));
+    }
+}
diff --git a/crates/capsule-core/src/config/mod.rs b/crates/capsule-core/src/config/mod.rs
index bf23c6b..46745de 100644
--- a/crates/capsule-core/src/config/mod.rs
+++ b/crates/capsule-core/src/config/mod.rs
@@ -1,3 +1,4 @@
 pub mod database;
+pub mod fingerprint;
 pub mod log;
 pub mod manifest;
diff --git a/crates/capsule-core/src/wasm/compiler/javascript.rs b/crates/capsule-core/src/wasm/compiler/javascript.rs
index f021120..0e3167d 100644
--- a/crates/capsule-core/src/wasm/compiler/javascript.rs
+++ b/crates/capsule-core/src/wasm/compiler/javascript.rs
@@ -3,6 +3,7 @@ use std::fs;
 use std::path::{Path, PathBuf};
 use std::process::{Command, Stdio};
 
+use crate::config::fingerprint::SourceFingerprint;
 use crate::wasm::utilities::introspection::javascript;
 use crate::wasm::utilities::wit_manager::WitManager;
 
@@ -97,7 +98,17 @@ impl JavascriptWasmCompiler {
     }
 
     pub fn compile_wasm(&self) -> Result<PathBuf, JavascriptWasmCompilerError> {
-        if !self.needs_rebuild(&self.source_path, &self.output_wasm)? {
+        let source_dir = self.source_path.parent().ok_or_else(|| {
+            JavascriptWasmCompilerError::FsError("Cannot determine source directory".to_string())
+        })?;
+
+        if !SourceFingerprint::needs_rebuild(
+            &self.cache_dir,
+            source_dir,
+            &self.output_wasm,
+            &["js", "ts", "toml"],
+            &["node_modules", "dist"],
+        ) {
             return Ok(self.output_wasm.clone());
         }
 
@@ -190,6 +201,13 @@ export const taskRunner = exports;
             )));
         }
 
+        let _ = SourceFingerprint::update_after_build(
+            &self.cache_dir,
+            source_dir,
+            &["js", "ts", "toml"],
+            &["node_modules", "dist"],
+        );
+
         Ok(self.output_wasm.clone())
     }
 
@@ -244,64 +262,6 @@ export const taskRunner = exports;
         ))
     }
 
-    fn needs_rebuild(
-        &self,
-        source: &Path,
-        output: &Path,
-    ) -> Result<bool, JavascriptWasmCompilerError> {
-        if !output.exists() {
-            return Ok(true);
-        }
-
-        let output_time = fs::metadata(output).and_then(|m| m.modified())?;
-
-        let source_time = fs::metadata(source).and_then(|m| m.modified())?;
-        if source_time > output_time {
-            return Ok(true);
-        }
-
-        if let Some(source_dir) = source.parent()
-            && Self::check_dir_modified(source_dir, source, output_time)?
-        {
-            return Ok(true);
-        }
-
-        Ok(false)
-    }
-
-    fn check_dir_modified(
-        dir: &Path,
-        source: &Path,
-        wasm_time: std::time::SystemTime,
-    ) -> Result<bool, JavascriptWasmCompilerError> {
-        if let Ok(entries) = fs::read_dir(dir) {
-            for entry in entries.flatten() {
-                let path = entry.path();
-
-                if path.is_dir() {
-                    let dir_name = path.file_name().and_then(|n| n.to_str()).unwrap_or("");
-                    if dir_name.starts_with('.') || dir_name == "node_modules" {
-                        continue;
-                    }
-
-                    if Self::check_dir_modified(&path, source, wasm_time)? {
-                        return Ok(true);
-                    }
-                } else if let Some(ext) = path.extension()
-                    && (ext == "js" || ext == "ts")
-                    && path != source
-                    && let Ok(metadata) = fs::metadata(&path)
-                    && let Ok(modified) = metadata.modified()
-                    && modified > wasm_time
-                {
-                    return Ok(true);
-                }
-            }
-        }
-
-        Ok(false)
-    }
-
     fn transpile_typescript(&self) -> Result<PathBuf, JavascriptWasmCompilerError> {
         let output_path = self.cache_dir.join(
             self.source_path
diff --git a/crates/capsule-core/src/wasm/compiler/python.rs b/crates/capsule-core/src/wasm/compiler/python.rs
index b16bb50..157c33c 100644
--- a/crates/capsule-core/src/wasm/compiler/python.rs
+++ b/crates/capsule-core/src/wasm/compiler/python.rs
@@ -5,6 +5,7 @@ use std::path::{Path, PathBuf};
 use std::process::Command;
 use std::process::Stdio;
 
+use crate::config::fingerprint::SourceFingerprint;
 use crate::wasm::utilities::introspection::python;
 use crate::wasm::utilities::wit_manager::WitManager;
 
@@ -90,7 +91,17 @@ impl PythonWasmCompiler {
     }
 
     pub fn compile_wasm(&self) -> Result<PathBuf, PythonWasmCompilerError> {
-        if !self.needs_rebuild(&self.source_path, &self.output_wasm)? {
+        let source_dir = self.source_path.parent().ok_or_else(|| {
+            PythonWasmCompilerError::FsError("Cannot determine source directory".to_string())
+        })?;
+
+        if !SourceFingerprint::needs_rebuild(
+            &self.cache_dir,
+            source_dir,
+            &self.output_wasm,
+            &["py", "toml"],
+            &["__pycache__"],
+        ) {
             return Ok(self.output_wasm.clone());
         }
 
@@ -177,64 +188,14 @@ from capsule.app import TaskRunner, exports
 
         self.cleanup_pycache(python_path);
 
-        Ok(self.output_wasm.clone())
-    }
-
-    fn needs_rebuild(
-        &self,
-        source: &Path,
-        wasm_path: &Path,
-    ) -> Result<bool, PythonWasmCompilerError> {
-        if !wasm_path.exists() {
-            return Ok(true);
-        }
-
-        let wasm_time = fs::metadata(wasm_path).and_then(|m| m.modified())?;
-
-        let source_time = fs::metadata(source).and_then(|m| m.modified())?;
-        if source_time > wasm_time {
-            return Ok(true);
-        }
-
-        if let Some(source_dir) = source.parent()
-            && Self::check_dir_modified(source_dir, source, wasm_time)?
-        {
-            return Ok(true);
-        }
-
-        Ok(false)
-    }
-
-    fn check_dir_modified(
-        dir: &Path,
-        source: &Path,
-        wasm_time: std::time::SystemTime,
-    ) -> Result<bool, PythonWasmCompilerError> {
-        if let Ok(entries) = fs::read_dir(dir) {
-            for entry in entries.flatten() {
-                let path = entry.path();
-
-                if path.is_dir() {
-                    let dir_name = path.file_name().and_then(|n| n.to_str()).unwrap_or("");
-                    if dir_name.starts_with('.') || dir_name == "__pycache__" {
-                        continue;
-                    }
-
-                    if Self::check_dir_modified(&path, source, wasm_time)? {
-                        return Ok(true);
-                    }
-                } else if path.extension().is_some_and(|ext| ext == "py")
-                    && path != source
-                    && let Ok(metadata) = fs::metadata(&path)
-                    && let Ok(modified) = metadata.modified()
-                    && modified > wasm_time
-                {
-                    return Ok(true);
-                }
-            }
-        }
+        let _ = SourceFingerprint::update_after_build(
+            &self.cache_dir,
+            source_dir,
+            &["py", "toml"],
+            &["__pycache__"],
+        );
 
-        Ok(false)
+        Ok(self.output_wasm.clone())
     }
 
     fn get_wit_path(&self) -> Result<PathBuf, PythonWasmCompilerError> {