diff --git a/tools/isobuild/compiler-plugin.js b/tools/isobuild/compiler-plugin.js
index 4646f3f76f..3ff6eb6463 100644
--- a/tools/isobuild/compiler-plugin.js
+++ b/tools/isobuild/compiler-plugin.js
@@ -670,46 +670,54 @@ export class PackageSourceBatch {
       scanner.addInputFiles(map.get(name));
 
       if (batch.useMeteorInstall) {
-        scanner.scanImports().getOutputFiles().forEach(file => {
-          if (file.missingNodeModules) {
-            _.extend(allMissingNodeModules, file.missingNodeModules);
-          }
-        });
+        scanner.scanImports();
+        _.extend(allMissingNodeModules, scanner.allMissingNodeModules);
       }
 
       scannerMap.set(name, scanner);
     });
 
-    const missingMap = new Map;
+    function handleMissing(missingNodeModules) {
+      const missingMap = new Map;
 
-    Object.keys(allMissingNodeModules).forEach(id => {
-      const parts = id.split("/");
-      let name = null;
+      Object.keys(missingNodeModules).forEach(id => {
+        const parts = id.split("/");
+        let name = null;
 
-      if (parts[0] === "meteor") {
-        if (parts.length > 2) {
-          name = parts[1];
-          parts[1] = ".";
-          id = parts.slice(1).join("/");
-        } else {
+        if (parts[0] === "meteor") {
+          if (parts.length > 2) {
+            name = parts[1];
+            parts[1] = ".";
+            id = parts.slice(1).join("/");
+          } else {
+            return;
+          }
+        }
+
+        if (! scannerMap.has(name)) {
           return;
         }
-      }
 
-      if (! scannerMap.has(name)) {
-        return;
-      }
+        if (missingMap.has(name)) {
+          missingMap.get(name).push(id);
+        } else {
+          missingMap.set(name, [id]);
+        }
+      });
 
-      if (missingMap.has(name)) {
-        missingMap.get(name).push(id);
-      } else {
-        missingMap.set(name, [id]);
-      }
-    });
+      const nextMissingNodeModules = Object.create(null);
 
-    missingMap.forEach((ids, name) => {
-      scannerMap.get(name).addNodeModules(ids);
-    });
+      missingMap.forEach((ids, name) => {
+        _.extend(nextMissingNodeModules,
+                 scannerMap.get(name).addNodeModules(ids));
+      });
+
+      if (! _.isEmpty(nextMissingNodeModules)) {
+        handleMissing(nextMissingNodeModules);
+      }
+    }
+
+    handleMissing(allMissingNodeModules);
 
     scannerMap.forEach((scanner, name) => {
       const isApp = ! name;
diff --git a/tools/isobuild/import-scanner.js b/tools/isobuild/import-scanner.js
index 8108e62462..390a851893 100644
--- a/tools/isobuild/import-scanner.js
+++ b/tools/isobuild/import-scanner.js
@@ -63,7 +63,8 @@ export default class ImportScanner {
     this.usedPackageNames = usedPackageNames;
     this.nodeModulesPath = nodeModulesPath;
     this.watchSet = watchSet;
-    this.absPathToOutputIndex = {};
+    this.absPathToOutputIndex = Object.create(null);
+    this.allMissingNodeModules = Object.create(null);
     this.outputFiles = [];
 
     this._statCache = new Map;
@@ -104,6 +105,8 @@ export default class ImportScanner {
   }
 
   addNodeModules(identifiers) {
+    const newMissingNodeModules = Object.create(null);
+
     if (identifiers) {
       if (typeof identifiers === "object" &&
           ! Array.isArray(identifiers)) {
@@ -111,17 +114,37 @@ export default class ImportScanner {
       }
 
       if (identifiers.length > 0) {
-        this._scanFile({
-          sourcePath: "fake.js",
-          // By specifying the .deps property of this fake file ahead of
-          // time, we can avoid calling findImportedModuleIdentifiers in the
-          // _scanFile method.
-          deps: identifiers,
-        });
+        const previousAllMissingNodeModules = this.allMissingNodeModules;
+        this.allMissingNodeModules = newMissingNodeModules;
+
+        try {
+          this._scanFile({
+            sourcePath: "fake.js",
+            // By specifying the .deps property of this fake file ahead of
+            // time, we can avoid calling findImportedModuleIdentifiers in the
+            // _scanFile method.
+            deps: identifiers,
+          });
+
+        } finally {
+          this.allMissingNodeModules = previousAllMissingNodeModules;
+
+          // Remove previously seen missing module identifiers from
+          // newMissingNodeModules and merge the new identifiers back into
+          // this.allMissingNodeModules.
+          each(keys(newMissingNodeModules), key => {
+            if (has(previousAllMissingNodeModules, key)) {
+              delete newMissingNodeModules[key];
+            } else {
+              previousAllMissingNodeModules[key] =
+                newMissingNodeModules[key];
+            }
+          });
+        }
       }
     }
 
-    return this;
+    return newMissingNodeModules;
   }
 
   getOutputFiles(options) {
@@ -476,7 +499,7 @@ export default class ImportScanner {
       // the top-level node_modules directory, and we should record the
       // missing dependency so that we can include it in the app bundle.
       const missing = file.missingNodeModules || Object.create(null);
-      missing[id] = true;
+      this.allMissingNodeModules[id] = missing[id] = true;
       file.missingNodeModules = missing;
     }