diff --git a/packages/cli-kit/src/public/node/custom-oclif-loader.ts b/packages/cli-kit/src/public/node/custom-oclif-loader.ts
index 750eb999ec..86116d7392 100644
--- a/packages/cli-kit/src/public/node/custom-oclif-loader.ts
+++ b/packages/cli-kit/src/public/node/custom-oclif-loader.ts
@@ -2,7 +2,7 @@ import {fileExistsSync} from './fs.js'
 import {cwd, joinPath, sniffForPath} from './path.js'
 import {isDevelopment} from './context/local.js'
 import {execaSync} from 'execa'
-import {Command, Config} from '@oclif/core'
+import {Config} from '@oclif/core'
 import {Options} from '@oclif/core/interfaces'
 
 export class ShopifyConfig extends Config {
@@ -17,6 +17,7 @@ export class ShopifyConfig extends Config {
       if (currentPathMightBeHydrogenMonorepo && !ignoreHydrogenMonorepo) {
         path = execaSync('npm', ['prefix']).stdout.trim()
       }
+
       if (fileExistsSync(joinPath(path, 'package.json'))) {
         // Hydrogen is bundled, but we still want to support loading it as an external plugin for two reasons:
         // 1. To allow users to use an older version of Hydrogen. (to not force upgrades)
@@ -25,69 +26,36 @@ export class ShopifyConfig extends Config {
           core: ['@shopify/cli-hydrogen'],
           path,
         }
+        // Force OCLIF to ignore manifests so commands are loaded dynamically
+        // to be replaced later
+        options.ignoreManifest = true
       }
     }
 
     super(options)
-
-    if (isDevelopment()) {
-      // @ts-expect-error: This is a private method that we are overriding. OCLIF doesn't provide a way to extend it.
-      // eslint-disable-next-line @typescript-eslint/unbound-method
-      this.determinePriority = this.customPriority
-    }
   }
 
-  customPriority(commands: Command.Loadable[]): Command.Loadable | undefined {
-    const oclifPlugins = this.pjson.oclif.plugins ?? []
-    const commandPlugins = commands.sort((aCommand, bCommand) => {
-      // eslint-disable-next-line no-restricted-syntax
-      const pluginAliasA = aCommand.pluginAlias ?? 'A-Cannot-Find-This'
-      // eslint-disable-next-line no-restricted-syntax
-      const pluginAliasB = bCommand.pluginAlias ?? 'B-Cannot-Find-This'
-      const aIndex = oclifPlugins.indexOf(pluginAliasA)
-      const bIndex = oclifPlugins.indexOf(pluginAliasB)
-
-      // If there is an external cli-hydrogen plugin, its commands should take priority over bundled ('core') commands
-      if (aCommand.pluginType === 'core' && bCommand.pluginAlias === '@shopify/cli-hydrogen') {
-        // If b is hydrogen and a is core sort b first
-        return 1
-      }
-
-      if (aCommand.pluginAlias === '@shopify/cli-hydrogen' && bCommand.pluginType === 'core') {
-        // If a is hydrogen and b is core sort a first
-        return -1
-      }
-
-      // All other cases are the default implementation from the private `determinePriority` method
-      // When both plugin types are 'core' plugins sort based on index
-      if (aCommand.pluginType === 'core' && bCommand.pluginType === 'core') {
-        // If b appears first in the pjson.plugins sort it first
-        return aIndex - bIndex
-      }
-
-      // if b is a core plugin and a is not sort b first
-      if (bCommand.pluginType === 'core' && aCommand.pluginType !== 'core') {
-        return 1
-      }
-
-      // if a is a core plugin and b is not sort a first
-      if (aCommand.pluginType === 'core' && bCommand.pluginType !== 'core') {
-        return -1
-      }
-
-      // if a is a jit plugin and b is not sort b first
-      if (aCommand.pluginType === 'jit' && bCommand.pluginType !== 'jit') {
-        return 1
-      }
+  async load(): Promise<void> {
+    await super.load()
 
-      // if b is a jit plugin and a is not sort a first
-      if (bCommand.pluginType === 'jit' && aCommand.pluginType !== 'jit') {
-        return -1
+    if (isDevelopment()) {
+      // Let OCLIF load all commands first, then manually replace bundled hydrogen
+      // commands with external ones after loading completes.
+      const externalHydrogenPlugin = Array.from(this.plugins.values()).find(
+        (plugin) => plugin.name === '@shopify/cli-hydrogen' && !plugin.isRoot,
+      )
+
+      if (externalHydrogenPlugin) {
+        for (const command of externalHydrogenPlugin.commands) {
+          if (command.id.startsWith('hydrogen')) {
+            // @ts-expect-error: _commands is private but we need to replace bundled commands
+            if (this._commands.has(command.id)) {
+              // @ts-expect-error: _commands is private but we need to replace bundled commands
+              this._commands.set(command.id, command)
+            }
+          }
+        }
       }
-
-      // neither plugin is core, so do not change the order
-      return 0
-    })
-    return commandPlugins[0]
+    }
   }
 }