diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a0a7c10b4..1020cddd4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -115,6 +115,14 @@ jobs:
         uses: ./.github/actions/build-cache
       - name: Test WASM
         run: cd sqlc-gen-ftl && cargo test --features ci --test sqlc_gen_ftl_test -- --nocapture
+      - name: Check for uncommitted changes
+        run: |
+          if [[ -n $(git status -s) ]]; then
+            echo "Error: Building sqlc-gen-ftl resulted in uncommitted changes:"
+            git status -s
+            git --no-pager diff
+            exit 1
+          fi
   extension:
     name: VSCode Extension
     runs-on: ubuntu-latest
diff --git a/Justfile b/Justfile
index 747161599..20ece3084 100644
--- a/Justfile
+++ b/Justfile
@@ -85,7 +85,7 @@ dev *args:
   watchexec -r {{WATCHEXEC_ARGS}} -- "ftl dev --plain {{args}}"
 
 # Build everything
-build-all: build-protos-unconditionally build-backend build-frontend build-backend-tests build-generate build-zips lsp-generate build-jvm build-language-plugins build-go2proto-testdata build-sqlc-gen-ftl
+build-all: build-protos-unconditionally build-backend build-frontend build-backend-tests build-generate build-zips lsp-generate build-jvm build-language-plugins build-go2proto-testdata
 
 # Run "go generate" on all packages
 build-generate:
@@ -165,16 +165,15 @@ build-extension: pnpm-install
   @mk {{EXTENSION_OUT}} : frontend/vscode/src frontend/vscode/package.json -- "cd frontend/vscode && rm -f ftl-*.vsix && pnpm run compile"
 
 # Build the sqlc-ftl-gen plugin, used to generate FTL schema from SQL
-build-sqlc-gen-ftl: build-protos
+build-sqlc-gen-ftl: build-rust-protos
     @mk {{SQLC_GEN_FTL_OUT}} : sqlc-gen-ftl/src -- \
         "cd sqlc-gen-ftl && \
         cargo build --target wasm32-wasip1 --release"
 
-cargo-install:
-    @mk sqlc-gen-ftl/target : sqlc-gen-ftl/Cargo.toml -- \
-        "cd sqlc-gen-ftl && \
-        cargo install protoc-gen-prost && \
-        cargo build"
+# Generate Rust protos
+build-rust-protos:
+    @mk sqlc-gen-ftl/src/protos : backend/protos -- \
+        "cd backend/protos && buf generate --template buf.gen.rust.yaml"
 
 # Install development version of VSCode extension
 install-extension: build-extension
diff --git a/backend/protos/buf.gen.rust.yaml b/backend/protos/buf.gen.rust.yaml
new file mode 100644
index 000000000..d802bbed1
--- /dev/null
+++ b/backend/protos/buf.gen.rust.yaml
@@ -0,0 +1,6 @@
+version: v1
+plugins:
+  - plugin: prost
+    out: src/protos
+    opt:
+      - bytes=.
diff --git a/backend/protos/buf.gen.yaml b/backend/protos/buf.gen.yaml
index b20b03964..dd8e9a876 100644
--- a/backend/protos/buf.gen.yaml
+++ b/backend/protos/buf.gen.yaml
@@ -16,7 +16,3 @@ plugins:
     out: ../../python-runtime/ftl/src/ftl/protos
     opt:
       - pyi_out=../../python-runtime/ftl/src/ftl/protos
-  - plugin: prost
-    out: ../../sqlc-gen-ftl/src/protos
-    opt:
-      - bytes=.
diff --git a/scripts/autofmt b/scripts/autofmt
index 6704b6b47..8360b0b9e 100755
--- a/scripts/autofmt
+++ b/scripts/autofmt
@@ -24,8 +24,6 @@ find backend/protos \( -name '*.pb.go' -o -name '*.connect.go' \) -print0 | xarg
 
 just pnpm-install
 
-just cargo-install
-
 (cd backend/protos && buf generate)
 
 echo "Formatting TypeScript..."