diff --git a/javascript/packages/orchestrator/src/configGenerator.ts b/javascript/packages/orchestrator/src/configGenerator.ts
index fc8720562..a7b478f45 100644
--- a/javascript/packages/orchestrator/src/configGenerator.ts
+++ b/javascript/packages/orchestrator/src/configGenerator.ts
@@ -16,7 +16,6 @@ import {
   DEFAULT_COLLATOR_IMAGE,
   DEFAULT_COMMAND,
   DEFAULT_CUMULUS_COLLATOR_BIN,
-  DEFAULT_GENESIS_GENERATE_SUBCOMMAND,
   DEFAULT_GLOBAL_TIMEOUT,
   DEFAULT_IMAGE,
   DEFAULT_KEYSTORE_KEY_TYPES,
@@ -357,9 +356,10 @@ export async function generateNetworkSpec(
           computedStatePath = genesisStatePath;
         }
       } else {
+        // NOTE: the subcommand to execute will be set later based on `substrateCliArgsVersion`.
         computedStateCommand = parachain.genesis_state_generator
           ? parachain.genesis_state_generator
-          : `${collatorBinary} ${DEFAULT_GENESIS_GENERATE_SUBCOMMAND}`;
+          : `${collatorBinary} {{GENESIS_GENERATE_SUBCOMMAND}}`;
 
         // TODO: we should remove this conditional ones
         // https://github.com/paritytech/polkadot-sdk/pull/2375 and
diff --git a/javascript/packages/orchestrator/src/constants.ts b/javascript/packages/orchestrator/src/constants.ts
index 27a4827f8..5c68f8ff6 100644
--- a/javascript/packages/orchestrator/src/constants.ts
+++ b/javascript/packages/orchestrator/src/constants.ts
@@ -41,6 +41,7 @@ const DEFAULT_CHAIN_SPEC_RAW = "{{chainName}}-raw.json";
 const DEFAULT_CHAIN_SPEC_COMMAND =
   "{{DEFAULT_COMMAND}} build-spec --chain {{chainName}} --disable-default-bootnode";
 const DEFAULT_GENESIS_GENERATE_SUBCOMMAND = "export-genesis-state";
+const DEFAULT_GENESIS_HEAD_GENERATE_SUBCOMMAND = "export-genesis-head";
 const DEFAULT_WASM_GENERATE_SUBCOMMAND = "export-genesis-wasm";
 const DEFAULT_ADDER_COLLATOR_BIN = "adder-collator";
 const UNDYING_COLLATOR_BIN = "undying-collator";
@@ -146,6 +147,7 @@ export {
   DEFAULT_CUMULUS_COLLATOR_BIN,
   DEFAULT_DATA_DIR,
   DEFAULT_GENESIS_GENERATE_SUBCOMMAND,
+  DEFAULT_GENESIS_HEAD_GENERATE_SUBCOMMAND,
   DEFAULT_GLOBAL_TIMEOUT,
   DEFAULT_IMAGE,
   DEFAULT_INDIVIDUAL_TEST_TIMEOUT,
diff --git a/javascript/packages/orchestrator/src/paras.ts b/javascript/packages/orchestrator/src/paras.ts
index 764f607b8..efeb4a8ea 100644
--- a/javascript/packages/orchestrator/src/paras.ts
+++ b/javascript/packages/orchestrator/src/paras.ts
@@ -4,6 +4,8 @@ import chainSpecFns, { isRawSpec } from "./chainSpec";
 import { getUniqueName } from "./configGenerator";
 import {
   DEFAULT_COLLATOR_IMAGE,
+  DEFAULT_GENESIS_GENERATE_SUBCOMMAND,
+  DEFAULT_GENESIS_HEAD_GENERATE_SUBCOMMAND,
   GENESIS_STATE_FILENAME,
   GENESIS_WASM_FILENAME,
   K8S_WAIT_UNTIL_SCRIPT_SUFIX,
@@ -225,10 +227,14 @@ export async function generateParachainFiles(
 
     const commands = [];
     if (parachain.genesisStateGenerator) {
-      let genesisStateGenerator = parachain.genesisStateGenerator.replace(
-        "{{CLIENT_REMOTE_DIR}}",
-        client.remoteDir as string,
-      );
+      const subcommand =
+        parachain.collators[0].substrateCliArgsVersion! >= 3
+          ? DEFAULT_GENESIS_HEAD_GENERATE_SUBCOMMAND
+          : DEFAULT_GENESIS_GENERATE_SUBCOMMAND;
+      let genesisStateGenerator = parachain.genesisStateGenerator
+        .replace("{{CLIENT_REMOTE_DIR}}", client.remoteDir as string)
+        .replace("{{GENESIS_GENERATE_SUBCOMMAND}}", subcommand);
+
       // cumulus
       if (parachain.cumulusBased) {
         const chainSpecPathInNode =
@@ -242,7 +248,7 @@ export async function generateParachainFiles(
         );
       }
 
-      if (client.providerName === "native" && !parachain.cumulusBased) {
+      if (client.providerName === "native" && parachain.cumulusBased) {
         // Inject a tmp base-path to prevent the use of a pre-existing un-purged data directory. This should only
         // be injected for `cumulus` base parachains.
         // See https://github.com/paritytech/zombienet/issues/1519
diff --git a/javascript/packages/orchestrator/src/providers/k8s/index.ts b/javascript/packages/orchestrator/src/providers/k8s/index.ts
index 237144014..1ef5b0cbf 100644
--- a/javascript/packages/orchestrator/src/providers/k8s/index.ts
+++ b/javascript/packages/orchestrator/src/providers/k8s/index.ts
@@ -6,7 +6,7 @@ import {
   genChaosDef,
 } from "./dynResourceDefinition";
 import { KubeClient, initClient } from "./kubeClient";
-import { getCliArgsVersion } from "./substrateCliArgsHelper";
+import { getCliArgsHelp } from "./substrateCliArgsHelper";
 
 export const provider = {
   KubeClient,
@@ -16,6 +16,6 @@ export const provider = {
   setupChainSpec,
   getChainSpecRaw,
   replaceNetworkRef,
-  getCliArgsVersion,
+  getCliArgsHelp,
   genChaosDef,
 };
diff --git a/javascript/packages/orchestrator/src/providers/k8s/substrateCliArgsHelper.ts b/javascript/packages/orchestrator/src/providers/k8s/substrateCliArgsHelper.ts
index e6bfd7d2c..a6ec910d7 100644
--- a/javascript/packages/orchestrator/src/providers/k8s/substrateCliArgsHelper.ts
+++ b/javascript/packages/orchestrator/src/providers/k8s/substrateCliArgsHelper.ts
@@ -1,19 +1,18 @@
-import { SubstrateCliArgsVersion } from "../../sharedTypes";
 import { getClient } from "../client";
 import { createTempNodeDef, genNodeDef } from "./dynResourceDefinition";
 import { KubeClient } from "./kubeClient";
 
-export const getCliArgsVersion = async (
+export const getCliArgsHelp = async (
   image: string,
   command: string,
-): Promise<SubstrateCliArgsVersion> => {
+): Promise<string> => {
   const client = getClient() as KubeClient;
-  // use echo to not finish the pod with error status.
+  // Use echo to not finish the pod with error status.
   const fullCmd = `${command} --help || echo ""`;
   const node = await createTempNodeDef(
     "temp",
     image,
-    "", // don't used
+    "", // Don't used
     fullCmd,
     false,
   );
@@ -23,11 +22,5 @@ export const getCliArgsVersion = async (
   await client.spawnFromDef(podDef);
   const logs = await client.getNodeLogs(podName);
 
-  if (logs.includes("--ws-port <PORT>")) {
-    return SubstrateCliArgsVersion.V0;
-  } else if (!logs.includes("--insecure-validator-i-know-what-i-do")) {
-    return SubstrateCliArgsVersion.V1;
-  } else {
-    return SubstrateCliArgsVersion.V2;
-  }
+  return logs;
 };
diff --git a/javascript/packages/orchestrator/src/providers/native/index.ts b/javascript/packages/orchestrator/src/providers/native/index.ts
index a215f17b7..316298418 100644
--- a/javascript/packages/orchestrator/src/providers/native/index.ts
+++ b/javascript/packages/orchestrator/src/providers/native/index.ts
@@ -5,7 +5,7 @@ import {
   replaceNetworkRef,
 } from "./dynResourceDefinition";
 import { NativeClient, initClient } from "./nativeClient";
-import { getCliArgsVersion } from "./substrateCliArgsHelper";
+import { getCliArgsHelp } from "./substrateCliArgsHelper";
 
 export const provider = {
   NativeClient,
@@ -15,5 +15,5 @@ export const provider = {
   setupChainSpec,
   getChainSpecRaw,
   replaceNetworkRef,
-  getCliArgsVersion,
+  getCliArgsHelp,
 };
diff --git a/javascript/packages/orchestrator/src/providers/native/substrateCliArgsHelper.ts b/javascript/packages/orchestrator/src/providers/native/substrateCliArgsHelper.ts
index 7ac24afb7..ab8b01372 100644
--- a/javascript/packages/orchestrator/src/providers/native/substrateCliArgsHelper.ts
+++ b/javascript/packages/orchestrator/src/providers/native/substrateCliArgsHelper.ts
@@ -1,20 +1,13 @@
-import { SubstrateCliArgsVersion } from "../../sharedTypes";
 import { getClient } from "../client";
 
-export const getCliArgsVersion = async (
+export const getCliArgsHelp = async (
   image: string,
   command: string,
-): Promise<SubstrateCliArgsVersion> => {
+): Promise<string> => {
   const client = getClient();
   const fullCmd = `${command} --help`;
   const logs = (await client.runCommand(["-c", fullCmd], { allowFail: true }))
     .stdout;
 
-  if (logs.includes("--ws-port <PORT>")) {
-    return SubstrateCliArgsVersion.V0;
-  } else if (!logs.includes("--insecure-validator-i-know-what-i-do")) {
-    return SubstrateCliArgsVersion.V1;
-  } else {
-    return SubstrateCliArgsVersion.V2;
-  }
+  return logs;
 };
diff --git a/javascript/packages/orchestrator/src/providers/podman/index.ts b/javascript/packages/orchestrator/src/providers/podman/index.ts
index 4e7354187..a6e511a72 100644
--- a/javascript/packages/orchestrator/src/providers/podman/index.ts
+++ b/javascript/packages/orchestrator/src/providers/podman/index.ts
@@ -5,7 +5,7 @@ import {
   replaceNetworkRef,
 } from "./dynResourceDefinition";
 import { PodmanClient, initClient } from "./podmanClient";
-import { getCliArgsVersion } from "./substrateCliArgsHelper";
+import { getCliArgsHelp } from "./substrateCliArgsHelper";
 
 export const provider = {
   PodmanClient,
@@ -15,5 +15,5 @@ export const provider = {
   setupChainSpec,
   getChainSpecRaw,
   replaceNetworkRef,
-  getCliArgsVersion,
+  getCliArgsHelp,
 };
diff --git a/javascript/packages/orchestrator/src/providers/podman/substrateCliArgsHelper.ts b/javascript/packages/orchestrator/src/providers/podman/substrateCliArgsHelper.ts
index 9fcd6a0a5..412800414 100644
--- a/javascript/packages/orchestrator/src/providers/podman/substrateCliArgsHelper.ts
+++ b/javascript/packages/orchestrator/src/providers/podman/substrateCliArgsHelper.ts
@@ -1,11 +1,10 @@
-import { SubstrateCliArgsVersion } from "../../sharedTypes";
 import { getClient } from "../client";
 import { createTempNodeDef, genNodeDef } from "./dynResourceDefinition";
 
-export const getCliArgsVersion = async (
+export const getCliArgsHelp = async (
   image: string,
   command: string,
-): Promise<SubstrateCliArgsVersion> => {
+): Promise<string> => {
   const client = getClient();
   const fullCmd = `${command} --help`;
   const node = await createTempNodeDef(
@@ -19,12 +18,5 @@ export const getCliArgsVersion = async (
   const podName = podDef.metadata.name;
   await client.spawnFromDef(podDef);
   const logs = await client.getNodeLogs(podName);
-
-  if (logs.includes("--ws-port <PORT>")) {
-    return SubstrateCliArgsVersion.V0;
-  } else if (!logs.includes("--insecure-validator-i-know-what-i-do")) {
-    return SubstrateCliArgsVersion.V1;
-  } else {
-    return SubstrateCliArgsVersion.V2;
-  }
+  return logs;
 };
diff --git a/javascript/packages/orchestrator/src/sharedTypes.ts b/javascript/packages/orchestrator/src/sharedTypes.ts
index e1ae4662d..9c4989c2f 100644
--- a/javascript/packages/orchestrator/src/sharedTypes.ts
+++ b/javascript/packages/orchestrator/src/sharedTypes.ts
@@ -5,6 +5,8 @@ export enum SubstrateCliArgsVersion {
   V1 = 1,
   // Includes the --insecure-validator-i-know-what-i-do flag.
   V2 = 2,
+  // Rename export-genesis-head to export-genesis-head in polkadot-parachain
+  V3 = 3,
 }
 
 // enums
diff --git a/javascript/packages/orchestrator/src/substrateCliArgsHelper.ts b/javascript/packages/orchestrator/src/substrateCliArgsHelper.ts
index e452d07da..988b87a96 100644
--- a/javascript/packages/orchestrator/src/substrateCliArgsHelper.ts
+++ b/javascript/packages/orchestrator/src/substrateCliArgsHelper.ts
@@ -2,12 +2,16 @@ import { series } from "@zombienet/utils";
 import { getProvider } from "./providers";
 import { Client } from "./providers/client";
 import { ComputedNetwork } from "./configTypes";
+import { SubstrateCliArgsVersion } from "./sharedTypes";
+import { Scope } from "./network";
+
+const debug = require("debug")("zombie::substrateCliArgsVersion");
 
 export const setSubstrateCliArgsVersion = async (
   network: ComputedNetwork,
   client: Client,
 ) => {
-  const { getCliArgsVersion } = getProvider(client.providerName);
+  const { getCliArgsHelp } = getProvider(client.providerName);
   // Calculate substrate cli version for each node
   // and set in the node to use later when we build the cmd.
   const imgCmdMap = new Map();
@@ -15,7 +19,11 @@ export const setSubstrateCliArgsVersion = async (
     if (node.substrateCliArgsVersion) return memo;
     const uniq_image_cmd = `${node.image}_${node.command}`;
     if (!memo.has(uniq_image_cmd))
-      memo.set(uniq_image_cmd, { image: node.image, command: node.command });
+      memo.set(uniq_image_cmd, {
+        image: node.image,
+        command: node.command,
+        scope: Scope.RELAY,
+      });
     return memo;
   }, imgCmdMap);
 
@@ -27,6 +35,7 @@ export const setSubstrateCliArgsVersion = async (
         memo.set(uniq_image_cmd, {
           image: collator.image,
           command: collator.command,
+          scope: Scope.PARA,
         });
     }
     return memo;
@@ -36,7 +45,8 @@ export const setSubstrateCliArgsVersion = async (
   const promiseGenerators = [];
   for (const [, v] of imgCmdMap) {
     const getVersionPromise = async () => {
-      const version = await getCliArgsVersion(v.image, v.command);
+      const helpStdout = await getCliArgsHelp(v.image, v.command);
+      const version = await getCliArgsVersion(helpStdout, v.scope);
       v.version = version;
       return version;
     };
@@ -61,3 +71,37 @@ export const setSubstrateCliArgsVersion = async (
     }
   }
 };
+
+function getCliArgsVersion(
+  helpStdout: string,
+  scope: Scope,
+): SubstrateCliArgsVersion {
+  // IFF stdout includes `ws-port` flag we are always in V0
+  if (helpStdout.includes("--ws-port <PORT>")) {
+    debug(`returning cliArgsVersion ${SubstrateCliArgsVersion.V0}`);
+    return SubstrateCliArgsVersion.V0;
+  }
+
+  // If not, we should check the scope
+  if (scope == Scope.RELAY) {
+    const version = !helpStdout.includes(
+      "--insecure-validator-i-know-what-i-do",
+    )
+      ? SubstrateCliArgsVersion.V1
+      : SubstrateCliArgsVersion.V2;
+
+    debug(`returning cliArgsVersion ${version}`);
+    return version;
+  } else if (scope == Scope.PARA) {
+    const version = !helpStdout.includes("export-genesis-head")
+      ? SubstrateCliArgsVersion.V2
+      : SubstrateCliArgsVersion.V3;
+
+    debug(`returning cliArgsVersion ${version}`);
+    return version;
+  } else {
+    debug(`returning default cliArgsVersion`);
+    // For other scopes we just return the latest version.
+    return SubstrateCliArgsVersion.V3;
+  }
+}