diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a697eef..ed80173 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -43,6 +43,9 @@ jobs:
       - name: Fetch MNIST model
         run: mise run fetch-mnist-rclone
 
+      - name: Prefetch dependencies
+        run: mise run prefetch
+
       - name: Build WASM modules
         run: mise run build-modules
 
diff --git a/.gitignore b/.gitignore
index 07cb91e..5fc6dbf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,5 @@ __pycache__/
 .pytest_cache/
 .python-version
 uv.lock
+node_modules/
+pnpm-lock.yaml
diff --git a/.mise.toml b/.mise.toml
index aa95113..c9f51ca 100644
--- a/.mise.toml
+++ b/.mise.toml
@@ -38,6 +38,7 @@ pipx = "latest"
 "pipx:cmake" = "latest"
 "pipx:componentize-py" = "latest"
 "pipx:pytest" = "latest"
+pnpm = "latest"
 protoc = "latest"
 python = "3.13"
 rclone = "latest"
@@ -154,7 +155,10 @@ depends = ["cargo-check"]
 run = "osv-scanner --lockfile Cargo.lock"
 
 [tasks.prefetch]
-depends = ["download-models"]
+# `build-ws-wasm-agent` produces `services/ws-wasm-agent/pkg/`, which the
+# static workspace references via a `link:` path. Run it before `pnpm install`
+# so the link target exists.
+depends = ["download-models", "build-ws-wasm-agent"]
 description = "Pre-download all dependencies and models (Rust crates, Dart packages, Python envs, Java/Maven, .NET, Node, WIT)"
 run = """
 cargo check --workspace
@@ -163,10 +167,16 @@ uv sync --directory services/ws-modules/pydata1
 uv sync --directory services/ws-modules/pyface1
 mvn dependency:resolve --quiet
 dotnet restore
-npm install --prefix services/ws-server/static
+pnpm install --dir services/ws-server/static --ignore-scripts --config.ignoredBuiltDependencies=protobufjs
 zig build --fetch --build-file services/ws-modules/zig-data1/build.zig
 """
 
+# pnpm refuses non-TTY destructive node_modules cleanup unless `CI=true`,
+# which fires when an earlier install left a different layout (e.g. before
+# `link:` was wired up). Treat `mise run prefetch` as a CI-style batch.
+[tasks.prefetch.env]
+CI = "true"
+
 [tasks.regenerate-verification]
 alias = "regen-verification"
 description = "Regenerate checked-in verification output files"
diff --git a/services/ws-server/Dockerfile b/services/ws-server/Dockerfile
index 1316d9a..608efcc 100644
--- a/services/ws-server/Dockerfile
+++ b/services/ws-server/Dockerfile
@@ -8,13 +8,20 @@ RUN apt-get update \
         npm \
         pkg-config \
         protobuf-compiler \
-    && rm -rf /var/lib/apt/lists/*
+    && rm -rf /var/lib/apt/lists/* \
+    && npm install -g pnpm
 
 WORKDIR /workspace
 
 COPY . .
 
-RUN npm install --omit=dev --prefix /workspace/runtime-deps onnxruntime-web pyodide
+# `--config.node-linker=hoisted` writes packages directly under
+# `node_modules/` instead of symlinking into `.pnpm/`, so the downstream
+# `COPY --from=builder /workspace/runtime-deps/node_modules/onnxruntime-web`
+# step picks up a real directory.
+RUN pnpm add --prod --dir /workspace/runtime-deps --config.node-linker=hoisted \
+        --ignore-scripts --config.ignoredBuiltDependencies=protobufjs \
+        onnxruntime-web pyodide
 RUN cargo build -p et-ws-server --release --locked
 
 FROM debian:bookworm-slim AS runtime
diff --git a/services/ws-server/static/package.json b/services/ws-server/static/package.json
index a5c124d..b8e23c4 100644
--- a/services/ws-server/static/package.json
+++ b/services/ws-server/static/package.json
@@ -9,7 +9,7 @@
     "style.css"
   ],
   "dependencies": {
-    "et-ws-wasm-agent": "*",
+    "et-ws-wasm-agent": "link:../../ws-wasm-agent/pkg",
     "onnxruntime-web": "*"
   }
 }