diff --git a/oak_functions/examples/benchmark/module/build.rs b/oak_functions/examples/benchmark/module/build.rs
index 06c43a93a84..b21694c5159 100644
--- a/oak_functions/examples/benchmark/module/build.rs
+++ b/oak_functions/examples/benchmark/module/build.rs
@@ -17,7 +17,7 @@
 extern crate prost_build;
 
 fn main() {
-    let file_paths = ["oak_functions/proto/benchmark.proto"];
+    let file_paths = ["proto/oak_functions/benchmark.proto"];
     prost_build::compile_protos(&file_paths, &["../../../../"]).expect("proto compilation failed");
 
     // Tell cargo to rerun this build script if the proto file has changed.
diff --git a/oak_functions_abi/README.md b/oak_functions_abi/README.md
index 8025420381a..35c7a9b4119 100644
--- a/oak_functions_abi/README.md
+++ b/oak_functions_abi/README.md
@@ -17,7 +17,7 @@ Oak Functions WebAssembly modules will typically use more convenient (and safer)
 wrappers from the higher-level [Oak Functions SDK](/oak_functions_sdk/).
 
 For a description of the API, see the
-[protobuf definition](/oak_functions_sdk/proto/oak_functions_wasm.proto).
+[protobuf definition](/proto/oak_functions/sdk/oak_functions_wasm.proto).
 
 ## Exported Functions
 
diff --git a/oak_functions_abi/build.rs b/oak_functions_abi/build.rs
index ecee3b7eb20..53594a16477 100644
--- a/oak_functions_abi/build.rs
+++ b/oak_functions_abi/build.rs
@@ -18,8 +18,8 @@ extern crate prost_build;
 
 fn main() {
     let file_paths = [
-        "oak_functions/proto/abi.proto",
-        "oak_functions/proto/lookup_data.proto",
+        "proto/oak_functions/abi.proto",
+        "proto/oak_functions/lookup_data.proto",
     ];
     prost_build::compile_protos(&file_paths, &[env!("WORKSPACE_ROOT")])
         .expect("proto compilation failed");
diff --git a/oak_functions_containers_app/build.rs b/oak_functions_containers_app/build.rs
index 777b96ce18e..047bf8e7f5e 100644
--- a/oak_functions_containers_app/build.rs
+++ b/oak_functions_containers_app/build.rs
@@ -22,7 +22,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         "../",
         &[
             "oak_crypto/proto/v1/crypto.proto",
-            "oak_functions_service/proto/oak_functions.proto",
+            "proto/oak_functions/service/oak_functions.proto",
         ],
         CodegenOptions {
             build_server: true,
diff --git a/oak_functions_containers_launcher/build.rs b/oak_functions_containers_launcher/build.rs
index 21d01095b05..3104660e48d 100644
--- a/oak_functions_containers_launcher/build.rs
+++ b/oak_functions_containers_launcher/build.rs
@@ -22,7 +22,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         "../",
         &[
             "oak_crypto/proto/v1/crypto.proto",
-            "oak_functions_service/proto/oak_functions.proto",
+            "proto/oak_functions/service/oak_functions.proto",
         ],
         CodegenOptions {
             build_client: true,
diff --git a/oak_functions_launcher/build.rs b/oak_functions_launcher/build.rs
index cb1a3018cff..5126dd67047 100644
--- a/oak_functions_launcher/build.rs
+++ b/oak_functions_launcher/build.rs
@@ -33,7 +33,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
     // Generate micro RPC code for exchanging messages with the enclave.
     micro_rpc_build::compile(
         &[format!(
-            "{}oak_functions_service/proto/oak_functions.proto",
+            "{}proto/oak_functions/service/oak_functions.proto",
             env!("WORKSPACE_ROOT")
         )],
         &[env!("WORKSPACE_ROOT")],
diff --git a/oak_functions_sdk/build.rs b/oak_functions_sdk/build.rs
index b21577a6c48..503d472344c 100644
--- a/oak_functions_sdk/build.rs
+++ b/oak_functions_sdk/build.rs
@@ -17,10 +17,10 @@
 fn main() {
     micro_rpc_build::compile(
         &[format!(
-            "{}oak_functions_sdk/proto/oak_functions_wasm.proto",
+            "{}proto/oak_functions/sdk/oak_functions_wasm.proto",
             env!("WORKSPACE_ROOT")
         )],
-        &[format!("{}oak_functions_sdk/proto", env!("WORKSPACE_ROOT"))],
+        &[format!("{}proto/oak_functions/sdk", env!("WORKSPACE_ROOT"))],
         Default::default(),
     );
 }
diff --git a/oak_functions_service/README.md b/oak_functions_service/README.md
index 50fb35256aa..9f3df4b39fc 100644
--- a/oak_functions_service/README.md
+++ b/oak_functions_service/README.md
@@ -8,7 +8,7 @@
 enclave binary.
 
 The interface of the service is defined via microRPC in
-[`oak_functions.proto`](/oak_functions_service/proto/oak_functions.proto).
+[`oak_functions.proto`](/proto/oak_functions/service/oak_functions.proto).
 
 # Lookup
 
diff --git a/oak_functions_service/build.rs b/oak_functions_service/build.rs
index bbc51172739..361764f4f11 100644
--- a/oak_functions_service/build.rs
+++ b/oak_functions_service/build.rs
@@ -19,7 +19,7 @@ use micro_rpc_build::ReceiverType;
 fn main() {
     micro_rpc_build::compile(
         &[format!(
-            "{}oak_functions_service/proto/oak_functions.proto",
+            "{}proto/oak_functions/service/oak_functions.proto",
             env!("WORKSPACE_ROOT")
         )],
         &[env!("WORKSPACE_ROOT")],
diff --git a/oak_functions_test_utils/src/lib.rs b/oak_functions_test_utils/src/lib.rs
index 3c4e15edab8..24abc58bdfc 100644
--- a/oak_functions_test_utils/src/lib.rs
+++ b/oak_functions_test_utils/src/lib.rs
@@ -73,7 +73,7 @@ pub fn compile_rust_wasm(manifest_path: &str, release: bool) -> anyhow::Result<V
 }
 
 /// Serializes the provided map as a contiguous buffer of length-delimited protobuf messages of type
-/// [`Entry`](https://github.com/project-oak/oak/blob/main/oak_functions/proto/lookup_data.proto).
+/// [`Entry`](https://github.com/project-oak/oak/blob/main/proto/oak_functions/lookup_data.proto).
 pub fn serialize_entries(entries: HashMap<Vec<u8>, Vec<u8>>) -> Vec<u8> {
     let mut buf = Vec::new();
     for (key, value) in entries.into_iter() {
diff --git a/oak_functions/proto/BUILD b/proto/oak_functions/BUILD
similarity index 100%
rename from oak_functions/proto/BUILD
rename to proto/oak_functions/BUILD
diff --git a/oak_functions/proto/abi.proto b/proto/oak_functions/abi.proto
similarity index 100%
rename from oak_functions/proto/abi.proto
rename to proto/oak_functions/abi.proto
diff --git a/oak_functions/proto/benchmark.proto b/proto/oak_functions/benchmark.proto
similarity index 100%
rename from oak_functions/proto/benchmark.proto
rename to proto/oak_functions/benchmark.proto
diff --git a/oak_functions/proto/lookup_data.proto b/proto/oak_functions/lookup_data.proto
similarity index 100%
rename from oak_functions/proto/lookup_data.proto
rename to proto/oak_functions/lookup_data.proto
diff --git a/oak_functions_sdk/proto/oak_functions_wasm.proto b/proto/oak_functions/sdk/oak_functions_wasm.proto
similarity index 100%
rename from oak_functions_sdk/proto/oak_functions_wasm.proto
rename to proto/oak_functions/sdk/oak_functions_wasm.proto
diff --git a/oak_functions_service/proto/oak_functions.proto b/proto/oak_functions/service/oak_functions.proto
similarity index 100%
rename from oak_functions_service/proto/oak_functions.proto
rename to proto/oak_functions/service/oak_functions.proto