diff --git a/README.md b/README.md
index c3a910b0..1a01f25e 100644
--- a/README.md
+++ b/README.md
@@ -229,6 +229,14 @@ Run `patch-package` without arguments to apply all patches in your project.
 
   Specify the name for the directory in which the patch files are located
 
+- `--ignore-missing`
+
+  Ignores patches for packages that are not present in node_modules.
+  This is useful when working with monorepos and wanting to install sub-packages
+  separately from the root package, with pruned dependencies.
+
+  See https://github.com/ds300/patch-package/issues/339 for background.
+
 #### Notes
 
 To apply patches individually, you may use `git`:
diff --git a/integration-tests/ignore-missing/__snapshots__/ignore-missing.test.ts.snap b/integration-tests/ignore-missing/__snapshots__/ignore-missing.test.ts.snap
new file mode 100644
index 00000000..a1b3ff33
--- /dev/null
+++ b/integration-tests/ignore-missing/__snapshots__/ignore-missing.test.ts.snap
@@ -0,0 +1,27 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`Test ignore-missing: patch-package returns 1 on missing package 1`] = `
+"SNAPSHOT: patch-package returns 1 on missing package
+Error: Patch file found for package missing-package which is not present at node_modules/missing-package
+---
+patch-package finished with 1 error(s).
+END SNAPSHOT"
+`;
+
+exports[`Test ignore-missing: adding --ignore-missing forces patch-package to return 0 1`] = `
+"SNAPSHOT: adding --ignore-missing forces patch-package to return 0
+patch-package 0.0.0
+Applying patches...
+left-pad@1.1.3 ✔
+Skipping missing missing-package@1.0.0 ✔
+END SNAPSHOT"
+`;
+
+exports[`Test ignore-missing: setting PATCH_PACKAGE_IGNORE_MISSING=1 forces patch-package to return 0 1`] = `
+"SNAPSHOT: setting PATCH_PACKAGE_IGNORE_MISSING=1 forces patch-package to return 0
+patch-package 0.0.0
+Applying patches...
+left-pad@1.1.3 ✔
+Skipping missing missing-package@1.0.0 ✔
+END SNAPSHOT"
+`;
diff --git a/integration-tests/ignore-missing/ignore-missing.sh b/integration-tests/ignore-missing/ignore-missing.sh
new file mode 100755
index 00000000..b44f60f5
--- /dev/null
+++ b/integration-tests/ignore-missing/ignore-missing.sh
@@ -0,0 +1,22 @@
+# make sure errors stop the script
+set -e
+
+echo "add patch-package"
+yarn add $1
+alias patch-package=./node_modules/.bin/patch-package
+
+(>&2 echo "SNAPSHOT: patch-package returns 1 on missing package")
+if patch-package;
+then
+  exit 1
+fi
+(>&2 echo "END SNAPSHOT")
+
+echo "SNAPSHOT: adding --ignore-missing forces patch-package to return 0"
+patch-package --ignore-missing;
+echo "END SNAPSHOT"
+
+export PATCH_PACKAGE_IGNORE_MISSING=1
+echo "SNAPSHOT: setting PATCH_PACKAGE_IGNORE_MISSING=1 forces patch-package to return 0"
+patch-package;
+echo "END SNAPSHOT"
diff --git a/integration-tests/ignore-missing/ignore-missing.test.ts b/integration-tests/ignore-missing/ignore-missing.test.ts
new file mode 100644
index 00000000..5b5b8717
--- /dev/null
+++ b/integration-tests/ignore-missing/ignore-missing.test.ts
@@ -0,0 +1,5 @@
+import { runIntegrationTest } from "../runIntegrationTest"
+runIntegrationTest({
+  projectName: "ignore-missing",
+  shouldProduceSnapshots: true,
+})
diff --git a/integration-tests/ignore-missing/package.json b/integration-tests/ignore-missing/package.json
new file mode 100644
index 00000000..287cde3b
--- /dev/null
+++ b/integration-tests/ignore-missing/package.json
@@ -0,0 +1,11 @@
+{
+  "name": "ignore-missing",
+  "version": "1.0.0",
+  "description": "integration test for patch-package",
+  "main": "index.js",
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "left-pad": "1.1.3"
+  }
+}
diff --git a/integration-tests/ignore-missing/patches/left-pad+1.1.3.patch b/integration-tests/ignore-missing/patches/left-pad+1.1.3.patch
new file mode 100644
index 00000000..0600ef9f
--- /dev/null
+++ b/integration-tests/ignore-missing/patches/left-pad+1.1.3.patch
@@ -0,0 +1,13 @@
+diff --git a/node_modules/left-pad/index.js b/node_modules/left-pad/index.js
+index 26f73ff..60f3f56 100644
+--- a/node_modules/left-pad/index.js
++++ b/node_modules/left-pad/index.js
+@@ -4,7 +4,7 @@
+      * To Public License, Version 2, as published by Sam Hocevar. See
+      * http://www.wtfpl.net/ for more details. */
+ 'use strict';
+-module.exports = leftPad;
++module.exports = patch-package;
+
+ var cache = [
+   '',
diff --git a/integration-tests/ignore-missing/patches/missing-package+1.0.0.patch b/integration-tests/ignore-missing/patches/missing-package+1.0.0.patch
new file mode 100644
index 00000000..e294d98b
--- /dev/null
+++ b/integration-tests/ignore-missing/patches/missing-package+1.0.0.patch
@@ -0,0 +1,13 @@
+diff --git a/node_modules/left-pad/index.js b/node_modules/left-pad/index.js
+index 26f73ff..60f3f56 100644
+--- a/node_modules/left-pad/index.js
++++ b/node_modules/left-pad/index.js
+@@ -7,7 +7,7 @@
+ module.exports = leftPad;
+
+ var cache = [
+-  '',
++  "",
+   ' ',
+   '  ',
+   '   ',
\ No newline at end of file
diff --git a/integration-tests/ignore-missing/yarn.lock b/integration-tests/ignore-missing/yarn.lock
new file mode 100644
index 00000000..392d269a
--- /dev/null
+++ b/integration-tests/ignore-missing/yarn.lock
@@ -0,0 +1,8 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+left-pad@1.1.3:
+  version "1.1.3"
+  resolved "https://registry.yarnpkg.com/left-pad/-/left-pad-1.1.3.tgz#612f61c033f3a9e08e939f1caebeea41b6f3199a"
+  integrity sha1-YS9hwDPzqeCOk58crr7qQbbzGZo=
diff --git a/src/applyPatches.ts b/src/applyPatches.ts
index 1a50d094..8627ff62 100644
--- a/src/applyPatches.ts
+++ b/src/applyPatches.ts
@@ -31,18 +31,23 @@ function getInstalledPackageVersion({
   pathSpecifier,
   isDevOnly,
   patchFilename,
+  ignoreMissing,
 }: {
   appPath: string
   path: string
   pathSpecifier: string
   isDevOnly: boolean
   patchFilename: string
+  ignoreMissing: boolean
 }): null | string {
   const packageDir = join(appPath, path)
   if (!existsSync(packageDir)) {
     if (process.env.NODE_ENV === "production" && isDevOnly) {
       return null
     }
+    if (ignoreMissing) {
+      return null
+    }
 
     let err =
       `${chalk.red("Error:")} Patch file found for package ${posix.basename(
@@ -98,6 +103,7 @@ export function applyPatchesForApp({
   shouldExitWithError,
   shouldExitWithWarning,
   bestEffort,
+  ignoreMissing,
 }: {
   appPath: string
   reverse: boolean
@@ -105,6 +111,7 @@ export function applyPatchesForApp({
   shouldExitWithError: boolean
   shouldExitWithWarning: boolean
   bestEffort: boolean
+  ignoreMissing: boolean
 }): void {
   const patchesDirectory = join(appPath, patchDir)
   const groupedPatches = getGroupedPatches(patchesDirectory)
@@ -128,6 +135,7 @@ export function applyPatchesForApp({
       warnings,
       errors,
       bestEffort,
+      ignoreMissing,
     })
   }
 
@@ -170,6 +178,7 @@ export function applyPatchesForPackage({
   warnings,
   errors,
   bestEffort,
+  ignoreMissing,
 }: {
   patches: PatchedPackageDetails[]
   appPath: string
@@ -178,6 +187,7 @@ export function applyPatchesForPackage({
   warnings: string[]
   errors: string[]
   bestEffort: boolean
+  ignoreMissing: boolean
 }) {
   const pathSpecifier = patches[0].pathSpecifier
   const state = patches.length > 1 ? getPatchApplicationState(patches[0]) : null
@@ -245,11 +255,12 @@ export function applyPatchesForPackage({
               patchDetails,
             })),
         patchFilename,
+        ignoreMissing,
       })
       if (!installedPackageVersion) {
-        // it's ok we're in production mode and this is a dev only package
+        // it's ok we're ignoring missing packages OR in production mode and this is a dev only package
         console.log(
-          `Skipping dev-only ${chalk.bold(
+          `Skipping ${ignoreMissing ? "missing" : "dev-only"} ${chalk.bold(
             pathSpecifier,
           )}@${version} ${chalk.blue("✔")}`,
         )
diff --git a/src/index.ts b/src/index.ts
index 8ee449a9..b2ac0c24 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -26,6 +26,7 @@ const argv = minimist(process.argv.slice(2), {
     "create-issue",
     "partial",
     "",
+    "ignore-missing",
   ],
   string: ["patch-dir", "append", "rebase"],
 })
@@ -115,6 +116,9 @@ if (argv.version || argv.v) {
 
     const shouldExitWithWarning = !!argv["error-on-warn"]
 
+    const ignoreMissing =
+      !!argv["ignore-missing"] || !!process.env.PATCH_PACKAGE_IGNORE_MISSING
+
     applyPatchesForApp({
       appPath,
       reverse,
@@ -122,6 +126,7 @@ if (argv.version || argv.v) {
       shouldExitWithError,
       shouldExitWithWarning,
       bestEffort: argv.partial,
+      ignoreMissing,
     })
   }
 }
@@ -178,13 +183,28 @@ Usage:
       and patch file updates (https://github.com/ds300/patch-package/issues/37),
       but might be useful in other contexts too.
       
+    ${chalk.bold("--ignore-missing")}
+
+      Ignores patches for packages that are not present in node_modules.
+      This is useful when working with monorepos and wanting to install sub-packages
+      separately from the root package, with pruned dependencies.
+
+      This option is can also be set via the environment variable
+      PATCH_PACKAGE_IGNORE_MISSING=1. Setting this env variable during the deployment
+      build process is recommended instead of using the --ignore-missing command option
+      when we want to ignore missing packages during deployment (of a monorepo with
+      pruned dependencies), but ensure we fail loudly during development if any
+      dependencies are moved or removed without updating the patches accordingly.
+
+      See https://github.com/ds300/patch-package/issues/339 for background.
+
 
   2. Creating patch files
   =======================
 
     ${chalk.bold("patch-package")} <package-name>${chalk.italic(
-    "[ <package-name>]",
-  )}
+      "[ <package-name>]",
+    )}
 
   When given package names as arguments, patch-package will create patch files
   based on any changes you've made to the versions installed by yarn/npm.