diff --git a/scripts/index-api.ts b/scripts/index-api.ts
index 73e09ae..8e86a03 100644
--- a/scripts/index-api.ts
+++ b/scripts/index-api.ts
@@ -1,3 +1,9 @@
+// MUST set environment variable before any imports that use @xenova/transformers
+// This prevents onnxruntime-node from being loaded on Alpine Linux (musl libc)
+if (process.env.TRANSFORMERS_BACKEND === 'wasm' || process.env.TRANSFORMERS_BACKEND === 'onnxruntime-web') {
+  process.env.ONNXRUNTIME_BACKEND = 'wasm';
+}
+
 import { ApiIndexer } from '../src/search/api-indexer.js';
 import path from 'path';
 
diff --git a/scripts/index-docs.ts b/scripts/index-docs.ts
index a6dd2f4..153b76b 100644
--- a/scripts/index-docs.ts
+++ b/scripts/index-docs.ts
@@ -1,5 +1,11 @@
 #!/usr/bin/env tsx
 
+// MUST set environment variable before any imports that use @xenova/transformers
+// This prevents onnxruntime-node from being loaded on Alpine Linux (musl libc)
+if (process.env.TRANSFORMERS_BACKEND === 'wasm' || process.env.TRANSFORMERS_BACKEND === 'onnxruntime-web') {
+  process.env.ONNXRUNTIME_BACKEND = 'wasm';
+}
+
 import { LanceDBIndexer, DocumentSource } from '../src/search/lancedb-indexer.js';
 import path from 'path';
 import { fileURLToPath } from 'url';
diff --git a/scripts/index-source.ts b/scripts/index-source.ts
index a74c1f8..4540fae 100644
--- a/scripts/index-source.ts
+++ b/scripts/index-source.ts
@@ -1,3 +1,9 @@
+// MUST set environment variable before any imports that use @xenova/transformers
+// This prevents onnxruntime-node from being loaded on Alpine Linux (musl libc)
+if (process.env.TRANSFORMERS_BACKEND === 'wasm' || process.env.TRANSFORMERS_BACKEND === 'onnxruntime-web') {
+  process.env.ONNXRUNTIME_BACKEND = 'wasm';
+}
+
 import { SourceCodeIndexer } from '../src/search/source-code-indexer.js';
 
 async function main() {
diff --git a/src/search/lancedb-indexer.ts b/src/search/lancedb-indexer.ts
index 7e72d2b..dd62ccc 100644
--- a/src/search/lancedb-indexer.ts
+++ b/src/search/lancedb-indexer.ts
@@ -58,13 +58,10 @@ export class LanceDBIndexer {
     console.log('Initializing LanceDB connection...');
     this.db = await connect(this.dbPath);
 
-    // Configure ONNX Runtime backend based on environment variable
-    // TRANSFORMERS_BACKEND=wasm for Alpine Linux (musl libc)
-    // Default: native ONNX Runtime (faster, requires glibc)
-    const backend = process.env.TRANSFORMERS_BACKEND;
-    if (backend === 'wasm' || backend === 'onnxruntime-web') {
+    // Log which backend is being used
+    const backend = process.env.ONNXRUNTIME_BACKEND;
+    if (backend === 'wasm') {
       console.log('Using WASM backend for Transformers.js (Alpine/musl compatibility mode)');
-      process.env.ONNXRUNTIME_BACKEND = 'wasm';
     } else {
       console.log('Using native ONNX Runtime backend (glibc required)');
     }