diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33aab2a233..642a7afbda 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,10 @@ Please add one entry in this file for each change in Yarn's behavior. Use the sa
 
   [#6983](https://github.com/yarnpkg/yarn/pull/6983) - [**Micha Reiser**](https://github.com/MichaReiser)
 
+- Run the engines check before executing `run` scripts.
+
+  [#7013](https://github.com/yarnpkg/yarn/issues/7013) - [**Eloy Durán**](https://github.com/alloy)
+
 ## 1.14.0
 
 - Improves PnP compatibility with Node 6
diff --git a/src/cli/commands/install.js b/src/cli/commands/install.js
index f273b5d3ed..e4aa6f3ea1 100644
--- a/src/cli/commands/install.js
+++ b/src/cli/commands/install.js
@@ -744,7 +744,7 @@ export class Install {
 
   async checkCompatibility(): Promise<void> {
     const {manifest} = await this.fetchRequestFromCwd();
-    await compatibility.checkOne({_reference: {}, ...manifest}, this.config, this.flags.ignoreEngines);
+    await compatibility.checkOne(manifest, this.config, this.flags.ignoreEngines);
   }
 
   async persistChanges(): Promise<void> {
diff --git a/src/cli/commands/run.js b/src/cli/commands/run.js
index 66fbaaff09..49a0270b8a 100644
--- a/src/cli/commands/run.js
+++ b/src/cli/commands/run.js
@@ -6,6 +6,7 @@ import {execCommand, makeEnv} from '../../util/execute-lifecycle-script.js';
 import {dynamicRequire} from '../../util/dynamic-require.js';
 import {MessageError} from '../../errors.js';
 import {registries} from '../../resolvers/index.js';
+import {checkOne as checkCompatibility} from '../../package-compatibility.js';
 import * as fs from '../../util/fs.js';
 import * as constants from '../../constants.js';
 
@@ -118,6 +119,13 @@ export async function run(config: Config, reporter: Reporter, flags: Object, arg
     }
 
     if (cmds.length) {
+      const ignoreEngines = !!(flags.ignoreEngines || config.getOption('ignore-engines'));
+      try {
+        await checkCompatibility(pkg, config, ignoreEngines);
+      } catch (err) {
+        throw err instanceof MessageError ? new MessageError(reporter.lang('cannotRunWithIncompatibleEnv')) : err;
+      }
+
       // Disable wrapper in executed commands
       process.env.YARN_WRAP_OUTPUT = 'false';
       for (const [stage, cmd] of cmds) {
diff --git a/src/package-compatibility.js b/src/package-compatibility.js
index 7ba68615d3..145f931094 100644
--- a/src/package-compatibility.js
+++ b/src/package-compatibility.js
@@ -8,7 +8,6 @@ import {entries} from './util/misc.js';
 import {version as yarnVersion} from './util/yarn-version.js';
 import {satisfiesWithPrereleases} from './util/semver.js';
 
-const invariant = require('invariant');
 const semver = require('semver');
 
 const VERSIONS = Object.assign({}, process.versions, {
@@ -111,9 +110,8 @@ export function checkOne(info: Manifest, config: Config, ignoreEngines: boolean)
 
   const pushError = msg => {
     const ref = info._reference;
-    invariant(ref, 'expected package reference');
 
-    if (ref.optional) {
+    if (ref && ref.optional) {
       ref.ignore = true;
       ref.incompatible = true;
 
diff --git a/src/reporters/lang/en.js b/src/reporters/lang/en.js
index fdd512fdd6..816446cdfd 100644
--- a/src/reporters/lang/en.js
+++ b/src/reporters/lang/en.js
@@ -229,11 +229,12 @@ const messages = {
   nodeGypAutoInstallFailed:
     'Failed to auto-install node-gyp. Please run "yarn global add node-gyp" manually. Error: $0',
 
-  foundIncompatible: 'Found incompatible module',
+  foundIncompatible: 'Found incompatible module.',
   incompatibleEngine: 'The engine $0 is incompatible with this module. Expected version $1. Got $2',
   incompatibleCPU: 'The CPU architecture $0 is incompatible with this module.',
   incompatibleOS: 'The platform $0 is incompatible with this module.',
   invalidEngine: 'The engine $0 appears to be invalid.',
+  cannotRunWithIncompatibleEnv: 'Commands cannot run with an incompatible environment.',
 
   optionalCompatibilityExcluded:
     '$0 is an optional dependency and failed compatibility check. Excluding it from installation.',