diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.assets.json b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.assets.json
index 37139758282cd..efd673ae6169d 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.assets.json
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.assets.json
@@ -40,7 +40,7 @@
         }
       }
     },
-    "55adc2a4d264e77d2c794df6cb13dd26ee0a9986d5b00a9bfe3cd48b6e0b2dfe": {
+    "db1c5d9623e5e22db4e511f52daf89f93fb1cbb8f325df40d03d5c50413e63a3": {
       "source": {
         "path": "integ-ec2-multiple-instances-in-stack.template.json",
         "packaging": "file"
@@ -48,7 +48,7 @@
       "destinations": {
         "current_account-current_region": {
           "bucketName": "cdk-hnb659fds-assets-${AWS::AccountId}-${AWS::Region}",
-          "objectKey": "55adc2a4d264e77d2c794df6cb13dd26ee0a9986d5b00a9bfe3cd48b6e0b2dfe.json",
+          "objectKey": "db1c5d9623e5e22db4e511f52daf89f93fb1cbb8f325df40d03d5c50413e63a3.json",
           "assumeRoleArn": "arn:${AWS::Partition}:iam::${AWS::AccountId}:role/cdk-hnb659fds-file-publishing-role-${AWS::AccountId}-${AWS::Region}"
         }
       }
diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.template.json b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.template.json
index 787b41606da14..e09958092be8c 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.template.json
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/integ-ec2-multiple-instances-in-stack.template.json
@@ -906,7 +906,7 @@
       "Fn::Join": [
        "",
        [
-        "#!/bin/bash\n# fingerprint: 8787022e9944cbeb\n(\n  set +e\n  /opt/aws/bin/cfn-init -v --region ",
+        "#!/bin/bash\n# fingerprint: 370d9b2dcf8bf44b\n(\n  set +e\n  /opt/aws/bin/cfn-init -v --region ",
         {
          "Ref": "AWS::Region"
         },
@@ -955,6 +955,29 @@
         "owner": "root",
         "group": "root"
        }
+      },
+      "commands": {
+       "000": {
+        "command": [
+         "useradd",
+         "-u",
+         "1001",
+         "-g",
+         "1001",
+         "eguser"
+        ]
+       },
+       "001": {
+        "command": [
+         "useradd",
+         "-a",
+         "-u",
+         "1001",
+         "-g",
+         "1001",
+         "eguser"
+        ]
+       }
       }
      }
     },
diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/manifest.json b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/manifest.json
index 9d805bac6514b..bd244eaf3c6a4 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/manifest.json
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/manifest.json
@@ -18,7 +18,7 @@
         "validateOnSynth": false,
         "assumeRoleArn": "arn:${AWS::Partition}:iam::${AWS::AccountId}:role/cdk-hnb659fds-deploy-role-${AWS::AccountId}-${AWS::Region}",
         "cloudFormationExecutionRoleArn": "arn:${AWS::Partition}:iam::${AWS::AccountId}:role/cdk-hnb659fds-cfn-exec-role-${AWS::AccountId}-${AWS::Region}",
-        "stackTemplateAssetObjectUrl": "s3://cdk-hnb659fds-assets-${AWS::AccountId}-${AWS::Region}/55adc2a4d264e77d2c794df6cb13dd26ee0a9986d5b00a9bfe3cd48b6e0b2dfe.json",
+        "stackTemplateAssetObjectUrl": "s3://cdk-hnb659fds-assets-${AWS::AccountId}-${AWS::Region}/db1c5d9623e5e22db4e511f52daf89f93fb1cbb8f325df40d03d5c50413e63a3.json",
         "requiresBootstrapStackVersion": 6,
         "bootstrapStackVersionSsmParameter": "/cdk-bootstrap/hnb659fds/version",
         "additionalDependencies": [
@@ -259,7 +259,10 @@
         "/integ-ec2-multiple-instances-in-stack/SecondInstance/Resource": [
           {
             "type": "aws:cdk:logicalId",
-            "data": "SecondInstance4834A636"
+            "data": "SecondInstance4834A636",
+            "trace": [
+              "!!DESTRUCTIVE_CHANGES: MAY_REPLACE"
+            ]
           }
         ],
         "/integ-ec2-multiple-instances-in-stack/BootstrapVersion": [
diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/tree.json b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/tree.json
index e556e0419844d..11c69d2c333ad 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/tree.json
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.js.snapshot/tree.json
@@ -1265,7 +1265,7 @@
                         "Fn::Join": [
                           "",
                           [
-                            "#!/bin/bash\n# fingerprint: 8787022e9944cbeb\n(\n  set +e\n  /opt/aws/bin/cfn-init -v --region ",
+                            "#!/bin/bash\n# fingerprint: 370d9b2dcf8bf44b\n(\n  set +e\n  /opt/aws/bin/cfn-init -v --region ",
                             {
                               "Ref": "AWS::Region"
                             },
diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.ts b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.ts
index 87a8ab87c74e6..de01a25b4715f 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.ts
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init-multiple.ts
@@ -55,6 +55,12 @@ class TestStack extends cdk.Stack {
               '/target/path/config.json',
               path.join(tmpDir, 'testConfigFile2'),
             ),
+            ec2.InitCommand.argvCommand([
+              'useradd', '-u', '1001', '-g', '1001', 'eguser',
+            ]),
+            ec2.InitCommand.argvCommand([
+              'useradd', '-a', '-u', '1001', '-g', '1001', 'eguser',
+            ]),
           ]),
         },
       }),
diff --git a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init.js.snapshot/manifest.json b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init.js.snapshot/manifest.json
index b0e1d19683224..e49e7eba966a3 100644
--- a/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init.js.snapshot/manifest.json
+++ b/packages/@aws-cdk-testing/framework-integ/test/aws-ec2/test/integ.instance-init.js.snapshot/manifest.json
@@ -199,7 +199,10 @@
         "/integ-init/Instance2/Resource": [
           {
             "type": "aws:cdk:logicalId",
-            "data": "Instance255F3526574cbd507dfce8b71"
+            "data": "Instance255F3526574cbd507dfce8b71",
+            "trace": [
+              "!!DESTRUCTIVE_CHANGES: WILL_DESTROY"
+            ]
           }
         ],
         "/integ-init/SsmParameterValue:--aws--service--ami-amazon-linux-latest--amzn-ami-hvm-x86_64-gp2:C96584B6-F00A-464E-AD19-53AFF4B05118.Parameter": [
@@ -219,15 +222,6 @@
             "type": "aws:cdk:logicalId",
             "data": "CheckBootstrapVersion"
           }
-        ],
-        "Instance255F35265a0c5f577d761edb0": [
-          {
-            "type": "aws:cdk:logicalId",
-            "data": "Instance255F35265a0c5f577d761edb0",
-            "trace": [
-              "!!DESTRUCTIVE_CHANGES: WILL_DESTROY"
-            ]
-          }
         ]
       },
       "displayName": "integ-init"
diff --git a/packages/aws-cdk-lib/aws-ec2/lib/cfn-init.ts b/packages/aws-cdk-lib/aws-ec2/lib/cfn-init.ts
index bf055b4b27a41..e97992612b233 100644
--- a/packages/aws-cdk-lib/aws-ec2/lib/cfn-init.ts
+++ b/packages/aws-cdk-lib/aws-ec2/lib/cfn-init.ts
@@ -311,10 +311,17 @@ function deepMerge(target?: Record<string, any>, src?: Record<string, any>) {
       if (target[key] && !Array.isArray(target[key])) {
         throw new Error(`Trying to merge array [${value}] into a non-array '${target[key]}'`);
       }
-      target[key] = Array.from(new Set([
-        ...target[key] ?? [],
-        ...value,
-      ]));
+      if (key === 'command') { // don't deduplicate command arguments
+        target[key] = new Array(
+          ...target[key] ?? [],
+          ...value,
+        );
+      } else {
+        target[key] = Array.from(new Set([
+          ...target[key] ?? [],
+          ...value,
+        ]));
+      }
       continue;
     }
     if (typeof value === 'object' && value) {
diff --git a/packages/aws-cdk-lib/aws-ec2/test/cfn-init.test.ts b/packages/aws-cdk-lib/aws-ec2/test/cfn-init.test.ts
index bf6823a598988..0a7f5f3a7181b 100644
--- a/packages/aws-cdk-lib/aws-ec2/test/cfn-init.test.ts
+++ b/packages/aws-cdk-lib/aws-ec2/test/cfn-init.test.ts
@@ -136,6 +136,68 @@ test('empty configs are not rendered', () => {
   });
 });
 
+test('duplicate config arguments not deduplicated', () => {
+  //GIVEN
+  const config = new ec2.InitConfig([
+    ec2.InitCommand.argvCommand([
+      'useradd', '-u', '1001', '-g', '1001', 'eguser',
+    ]),
+    ec2.InitCommand.argvCommand([
+      'useradd', '-a', '-u', '1001', '-g', '1001', 'eguser',
+    ]),
+  ]);
+
+  // WHEN
+  const init = ec2.CloudFormationInit.fromConfigSets({
+    configSets: { default: ['config'] },
+    configs: { config },
+  });
+  init.attach(resource, linuxOptions());
+
+  // THEN
+  expectMetadataLike({
+    'AWS::CloudFormation::Init': {
+      configSets: {
+        default: ['config'],
+      },
+      config: {
+        commands: {
+          '000': {
+            command: ['useradd', '-u', '1001', '-g', '1001', 'eguser'],
+          },
+          '001': {
+            command: ['useradd', '-a', '-u', '1001', '-g', '1001', 'eguser'],
+          },
+        },
+      },
+    },
+  });
+});
+
+test('deepMerge properly deduplicates non-command arguments', () => {
+  // WHEN
+  const config = new ec2.InitConfig([
+    ec2.InitSource.fromUrl('/tmp/blinky', 'https://amazon.com/blinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/blinky', 'https://amazon.com/blinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/pinky', 'https://amazon.com/pinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/pinky', 'https://amazon.com/pinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/inky', 'https://amazon.com/inky.zip'),
+    ec2.InitSource.fromUrl('/tmp/clyde', 'https://amazon.com/blinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/clyde', 'https://amazon.com/blinky.zip'),
+    ec2.InitSource.fromUrl('/tmp/clyde', 'https://amazon.com/blinky.zip'),
+  ]);
+
+  // THEN
+  expect(config._bind(stack, linuxOptions()).config).toEqual(expect.objectContaining({
+    sources: {
+      '/tmp/blinky': 'https://amazon.com/blinky.zip',
+      '/tmp/pinky': 'https://amazon.com/pinky.zip',
+      '/tmp/inky': 'https://amazon.com/inky.zip',
+      '/tmp/clyde': 'https://amazon.com/blinky.zip',
+    },
+  }));
+});
+
 describe('userdata', () => {
   let simpleInit: ec2.CloudFormationInit;
   beforeEach(() => {