diff --git a/.changeset/spotty-badgers-attack.md b/.changeset/spotty-badgers-attack.md
new file mode 100644
index 00000000000..82427d97e59
--- /dev/null
+++ b/.changeset/spotty-badgers-attack.md
@@ -0,0 +1,5 @@
+---
+'@shopify/theme': patch
+---
+
+Improve Glob Pattern subdirectory mismatch error handling
diff --git a/packages/theme/src/cli/utilities/asset-ignore.test.ts b/packages/theme/src/cli/utilities/asset-ignore.test.ts
index 58b08e4565b..3ec68a08928 100644
--- a/packages/theme/src/cli/utilities/asset-ignore.test.ts
+++ b/packages/theme/src/cli/utilities/asset-ignore.test.ts
@@ -1,5 +1,6 @@
 import {applyIgnoreFilters} from './asset-ignore.js'
 import {ReadOptions, fileExists, readFile} from '@shopify/cli-kit/node/fs'
+import {outputWarn} from '@shopify/cli-kit/node/output'
 import {joinPath} from '@shopify/cli-kit/node/path'
 import {test, describe, beforeEach, vi, expect} from 'vitest'
 
@@ -14,6 +15,7 @@ vi.mock('@shopify/cli-kit/node/fs', async () => {
 })
 
 vi.mock('@shopify/cli-kit/node/path')
+vi.mock('@shopify/cli-kit/node/output')
 
 describe('applyIgnoreFilters', () => {
   const checksums = [
@@ -129,4 +131,35 @@ describe('applyIgnoreFilters', () => {
       {key: 'templates/customers/account.json', checksum: '7777777777777777777777777777777'},
     ])
   })
+
+  test(`only outputs glob pattern subdirectory warnings for the templates folder`, async () => {
+    // Given
+    const options = {only: ['assets/*.json', 'config/*.json', 'sections/*.json']}
+    // When
+    await applyIgnoreFilters(checksums, themeFileSystem, options)
+    // Then
+    expect(vi.mocked(outputWarn)).not.toHaveBeenCalled()
+  })
+
+  test(`outputs warnings when there are glob pattern modifications required for subdirectories`, async () => {
+    // Given
+    const options = {only: ['templates/*.json']}
+
+    // When
+    await applyIgnoreFilters(checksums, themeFileSystem, options)
+
+    // Then
+    expect(vi.mocked(outputWarn)).toHaveBeenCalledTimes(1)
+  })
+
+  test('only outputs a single warning for duplicated glob patterns', async () => {
+    // Given
+    const options = {only: ['templates/*.json'], ignore: ['templates/*.json']}
+
+    // When
+    await applyIgnoreFilters(checksums, themeFileSystem, options)
+
+    // Then
+    expect(vi.mocked(outputWarn)).toHaveBeenCalledTimes(1)
+  })
 })
diff --git a/packages/theme/src/cli/utilities/asset-ignore.ts b/packages/theme/src/cli/utilities/asset-ignore.ts
index 581a1d94a1a..cdf335a6da5 100644
--- a/packages/theme/src/cli/utilities/asset-ignore.ts
+++ b/packages/theme/src/cli/utilities/asset-ignore.ts
@@ -12,15 +12,20 @@ export async function applyIgnoreFilters(
 ) {
   const shopifyIgnore = await shopifyIgnoredPatterns(themeFileSystem)
 
+  const ignoreOptions = options.ignore ?? []
+  const onlyOptions = options.only ?? []
+
+  raiseWarningForNonExplicitGlobPatterns([...shopifyIgnore, ...ignoreOptions, ...onlyOptions])
+
   return themeChecksums
     .filter(filterBy(shopifyIgnore, '.shopifyignore'))
-    .filter(filterBy(options.ignore, '--ignore'))
-    .filter(filterBy(options.only, '--only', true))
+    .filter(filterBy(ignoreOptions, '--ignore'))
+    .filter(filterBy(onlyOptions, '--only', true))
 }
 
-function filterBy(patterns: string[] | undefined, type: string, invertMatch = false) {
+function filterBy(patterns: string[], type: string, invertMatch = false) {
   return ({key}: Checksum) => {
-    if (!patterns) return true
+    if (patterns.length === 0) return true
 
     const match = patterns.some((pattern) => matchGlob(key, pattern) || regexMatch(key, pattern))
     const shouldIgnore = invertMatch ? !match : match
@@ -56,14 +61,31 @@ function matchGlob(key: string, pattern: string) {
   // When the the standard match fails and the pattern includes '/*.', we
   // replace '/*.' with '/**/*.' to emulate Shopify CLI 2.x behavior, as it was
   // based on 'File.fnmatch'.
-  if (pattern.includes('/*.')) {
-    outputWarn(`The pattern ${pattern} is unsafe, please use a valid regex or glob.`)
+  if (shouldReplaceGlobPattern(pattern)) {
     return originalMatchGlob(key, pattern.replace('/*.', '/**/*.'))
   }
 
   return false
 }
 
+function raiseWarningForNonExplicitGlobPatterns(patterns: string[]) {
+  const allPatterns = new Set(patterns)
+  allPatterns.forEach((pattern) => {
+    if (shouldReplaceGlobPattern(pattern)) {
+      outputWarn(
+        `Warning: The pattern '${pattern}' does not include subdirectories. To maintain backwards compatibility, we have modified your pattern to ${pattern.replace(
+          '/*.',
+          '/**/*.',
+        )} to explicitly include subdirectories.`,
+      )
+    }
+  })
+}
+
+function shouldReplaceGlobPattern(pattern: string): boolean {
+  return pattern.includes('/*.') && !pattern.includes('/**/*.') && pattern.includes('templates/')
+}
+
 function regexMatch(key: string, pattern: string) {
   try {
     return key.match(pattern)