diff --git a/backend/package.json b/backend/package.json
index 4cfe0dc..dcb7ae3 100644
--- a/backend/package.json
+++ b/backend/package.json
@@ -15,7 +15,10 @@
     "db:migrate": "ts-node src/scripts/setup-database.ts",
     "db:seed": "ts-node src/models/seed.ts",
     "db:setup": "npm run db:migrate && node scripts/setup_supabase.js",
-    "deploy:firebase": "npm run build && firebase deploy --only functions",
+    "pre-deploy-check": "bash scripts/pre-deploy-check.sh",
+    "clean-env-secrets": "bash scripts/clean-env-secrets.sh",
+    "deploy:firebase": "npm run pre-deploy-check && npm run build && firebase deploy --only functions",
+    "deploy:firebase:force": "npm run build && firebase deploy --only functions",
     "deploy:cloud-run": "npm run build && gcloud run deploy cim-processor-backend --source . --region us-central1 --platform managed --allow-unauthenticated",
     "deploy:docker": "npm run build && docker build -t cim-processor-backend . && docker run -p 8080:8080 cim-processor-backend",
     "docker:build": "docker build -t cim-processor-backend .",
@@ -23,6 +26,7 @@
     "emulator": "firebase emulators:start --only functions",
     "emulator:ui": "firebase emulators:start --only functions --ui",
     "sync:config": "./scripts/sync-firebase-config.sh",
+    "sync-secrets": "ts-node src/scripts/sync-firebase-secrets-to-env.ts",
     "diagnose": "ts-node src/scripts/comprehensive-diagnostic.ts",
     "test:linkage": "ts-node src/scripts/test-linkage.ts",
     "test:postgres": "ts-node src/scripts/test-postgres-connection.ts",
diff --git a/backend/scripts/clean-env-secrets.sh b/backend/scripts/clean-env-secrets.sh
new file mode 100755
index 0000000..343cb0c
--- /dev/null
+++ b/backend/scripts/clean-env-secrets.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+# Remove secrets from .env file that should only be Firebase Secrets
+# This prevents conflicts during deployment
+
+set -e
+
+if [ ! -f .env ]; then
+  echo "No .env file found"
+  exit 0
+fi
+
+# List of secrets to remove from .env
+SECRETS=(
+  "ANTHROPIC_API_KEY"
+  "OPENAI_API_KEY"
+  "OPENROUTER_API_KEY"
+  "DATABASE_URL"
+  "SUPABASE_SERVICE_KEY"
+  "SUPABASE_ANON_KEY"
+  "EMAIL_PASS"
+)
+
+echo "🧹 Cleaning secrets from .env file..."
+
+BACKUP_FILE=".env.pre-clean-$(date +%Y%m%d-%H%M%S).bak"
+cp .env "$BACKUP_FILE"
+echo "📋 Backup created: $BACKUP_FILE"
+
+REMOVED=0
+for secret in "${SECRETS[@]}"; do
+  if grep -q "^${secret}=" .env; then
+    # Remove the line (including commented versions)
+    sed -i.tmp "/^#*${secret}=/d" .env
+    rm -f .env.tmp
+    echo "  ✅ Removed ${secret}"
+    REMOVED=$((REMOVED + 1))
+  fi
+done
+
+if [ $REMOVED -gt 0 ]; then
+  echo ""
+  echo "✅ Removed ${REMOVED} secret(s) from .env"
+  echo "💡 For local development, use: npm run sync-secrets"
+else
+  echo "✅ No secrets found in .env (already clean)"
+  rm "$BACKUP_FILE"
+fi
+
diff --git a/backend/scripts/pre-deploy-check.sh b/backend/scripts/pre-deploy-check.sh
new file mode 100755
index 0000000..c8c3361
--- /dev/null
+++ b/backend/scripts/pre-deploy-check.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+# Pre-deployment validation script
+# Checks for environment variable conflicts before deploying Firebase Functions
+
+set -e
+
+echo "🔍 Pre-deployment validation..."
+
+# List of secrets that should NOT be in .env
+SECRETS=(
+  "ANTHROPIC_API_KEY"
+  "OPENAI_API_KEY"
+  "OPENROUTER_API_KEY"
+  "DATABASE_URL"
+  "SUPABASE_SERVICE_KEY"
+  "SUPABASE_ANON_KEY"
+  "EMAIL_PASS"
+)
+
+CONFLICTS=0
+
+if [ -f .env ]; then
+  echo "Checking .env file for secret conflicts..."
+  
+  for secret in "${SECRETS[@]}"; do
+    if grep -q "^${secret}=" .env; then
+      echo "⚠️  CONFLICT: ${secret} is in .env but should only be a Firebase Secret"
+      CONFLICTS=$((CONFLICTS + 1))
+    fi
+  done
+  
+  if [ $CONFLICTS -gt 0 ]; then
+    echo ""
+    echo "❌ Found ${CONFLICTS} conflict(s). Please remove these from .env:"
+    echo ""
+    echo "For local development, use: npm run sync-secrets"
+    echo "This will temporarily add secrets to .env for local testing."
+    echo ""
+    echo "To fix now, run: npm run clean-env-secrets"
+    exit 1
+  fi
+else
+  echo "✅ No .env file found (this is fine for deployment)"
+fi
+
+echo "✅ Pre-deployment check passed!"
+exit 0
+