diff --git a/apps/v4/public/r/styles/new-york-v4/index.json b/apps/v4/public/r/styles/new-york-v4/index.json
index ae7203d2fe..69f13cef90 100644
--- a/apps/v4/public/r/styles/new-york-v4/index.json
+++ b/apps/v4/public/r/styles/new-york-v4/index.json
@@ -16,7 +16,16 @@
   "files": [],
   "cssVars": {},
   "css": {
-    "@import \"shadcn/tailwind.css\"": {}
+    "@import \"tw-animate-css\"": {},
+    "@import \"shadcn/tailwind.css\"": {},
+    "@layer base": {
+      "*": {
+        "@apply border-border outline-ring/50": {}
+      },
+      "body": {
+        "@apply bg-background text-foreground": {}
+      }
+    }
   },
   "type": "registry:style"
 }
\ No newline at end of file
diff --git a/apps/v4/public/r/styles/new-york-v4/registry.json b/apps/v4/public/r/styles/new-york-v4/registry.json
index 7b72e315e2..2db23814c3 100644
--- a/apps/v4/public/r/styles/new-york-v4/registry.json
+++ b/apps/v4/public/r/styles/new-york-v4/registry.json
@@ -19,7 +19,16 @@
       "files": [],
       "cssVars": {},
       "css": {
-        "@import \"shadcn/tailwind.css\"": {}
+        "@import \"tw-animate-css\"": {},
+        "@import \"shadcn/tailwind.css\"": {},
+        "@layer base": {
+          "*": {
+            "@apply border-border outline-ring/50": {}
+          },
+          "body": {
+            "@apply bg-background text-foreground": {}
+          }
+        }
       },
       "type": "registry:style"
     },
@@ -40,7 +49,16 @@
       "files": [],
       "cssVars": {},
       "css": {
-        "@import \"shadcn/tailwind.css\"": {}
+        "@import \"tw-animate-css\"": {},
+        "@import \"shadcn/tailwind.css\"": {},
+        "@layer base": {
+          "*": {
+            "@apply border-border outline-ring/50": {}
+          },
+          "body": {
+            "@apply bg-background text-foreground": {}
+          }
+        }
       },
       "type": "registry:style"
     },
diff --git a/apps/v4/public/r/styles/new-york-v4/style.json b/apps/v4/public/r/styles/new-york-v4/style.json
index 452a4322f8..9d8bb6576c 100644
--- a/apps/v4/public/r/styles/new-york-v4/style.json
+++ b/apps/v4/public/r/styles/new-york-v4/style.json
@@ -16,7 +16,16 @@
   "files": [],
   "cssVars": {},
   "css": {
-    "@import \"shadcn/tailwind.css\"": {}
+    "@import \"tw-animate-css\"": {},
+    "@import \"shadcn/tailwind.css\"": {},
+    "@layer base": {
+      "*": {
+        "@apply border-border outline-ring/50": {}
+      },
+      "body": {
+        "@apply bg-background text-foreground": {}
+      }
+    }
   },
   "type": "registry:style"
 }
\ No newline at end of file
diff --git a/apps/v4/registry/new-york-v4/registry.ts b/apps/v4/registry/new-york-v4/registry.ts
index d9a5b99690..ce71657675 100644
--- a/apps/v4/registry/new-york-v4/registry.ts
+++ b/apps/v4/registry/new-york-v4/registry.ts
@@ -26,7 +26,16 @@ const NEW_YORK_V4_STYLE = {
   devDependencies: ["tw-animate-css", "shadcn"],
   registryDependencies: ["utils"],
   css: {
+    '@import "tw-animate-css"': {},
     '@import "shadcn/tailwind.css"': {},
+    "@layer base": {
+      "*": {
+        "@apply border-border outline-ring/50": {},
+      },
+      body: {
+        "@apply bg-background text-foreground": {},
+      },
+    },
   },
   cssVars: {},
   files: [],
diff --git a/packages/shadcn/src/commands/add.ts b/packages/shadcn/src/commands/add.ts
index ebfb821a5d..e2cc919418 100644
--- a/packages/shadcn/src/commands/add.ts
+++ b/packages/shadcn/src/commands/add.ts
@@ -90,20 +90,19 @@ export const add = new Command()
       }
 
       let itemType: z.infer<typeof registryItemTypeSchema> | undefined
-      let shouldInstallBaseStyle = true
+      let shouldInstallStyleIndex = true
       if (components.length > 0) {
         const [registryItem] = await getRegistryItems([components[0]], {
           config: initialConfig,
         })
         itemType = registryItem?.type
-        shouldInstallBaseStyle =
-          itemType !== "registry:theme" && itemType !== "registry:style"
+        shouldInstallStyleIndex =
+          itemType !== "registry:theme" &&
+          itemType !== "registry:style" &&
+          itemType !== "registry:base"
 
         if (isUniversalRegistryItem(registryItem)) {
-          await addComponents(components, initialConfig, {
-            ...options,
-            baseStyle: shouldInstallBaseStyle,
-          })
+          await addComponents(components, initialConfig, options)
           return
         }
 
@@ -180,8 +179,8 @@ export const add = new Command()
           isNewProject: false,
           srcDir: options.srcDir,
           cssVariables: options.cssVariables,
-          baseStyle: shouldInstallBaseStyle,
-          baseColor: shouldInstallBaseStyle ? undefined : "neutral",
+          installStyleIndex: shouldInstallStyleIndex,
+          baseColor: shouldInstallStyleIndex ? undefined : "neutral",
           components: options.components,
         })
         initHasRun = true
@@ -216,8 +215,8 @@ export const add = new Command()
             isNewProject: true,
             srcDir: options.srcDir,
             cssVariables: options.cssVariables,
-            baseStyle: shouldInstallBaseStyle,
-            baseColor: shouldInstallBaseStyle ? undefined : "neutral",
+            installStyleIndex: shouldInstallStyleIndex,
+            baseColor: shouldInstallStyleIndex ? undefined : "neutral",
             components: options.components,
           })
           initHasRun = true
@@ -244,10 +243,7 @@ export const add = new Command()
       config = updatedConfig
 
       if (!initHasRun) {
-        await addComponents(options.components, config, {
-          ...options,
-          baseStyle: shouldInstallBaseStyle,
-        })
+        await addComponents(options.components, config, options)
       }
 
       // If we're adding a single component and it's from the v0 registry,
diff --git a/packages/shadcn/src/commands/create.ts b/packages/shadcn/src/commands/create.ts
index 53027d9515..53357cf6b4 100644
--- a/packages/shadcn/src/commands/create.ts
+++ b/packages/shadcn/src/commands/create.ts
@@ -204,7 +204,7 @@ export const create = new Command()
         rtl: opts.rtl,
         template,
         baseColor,
-        baseStyle: false,
+        installStyleIndex: false,
         registryBaseConfig,
         skipPreflight: false,
       })
@@ -218,7 +218,6 @@ export const create = new Command()
           components.push("direction")
         }
         await addComponents(components, config, {
-          baseStyle: false,
           silent: true,
           overwrite: true,
         })
diff --git a/packages/shadcn/src/commands/init.ts b/packages/shadcn/src/commands/init.ts
index 9b12cd81f1..86abfbbab9 100644
--- a/packages/shadcn/src/commands/init.ts
+++ b/packages/shadcn/src/commands/init.ts
@@ -104,7 +104,7 @@ export const initOptionsSchema = z.object({
         ).join("', '")}'`,
       }
     ),
-  baseStyle: z.boolean(),
+  installStyleIndex: z.boolean(),
   // Config from registry:base item to merge into components.json.
   registryBaseConfig: rawConfigSchema.deepPartial().optional(),
 })
@@ -157,6 +157,7 @@ export const init = new Command()
         isNewProject: false,
         components,
         ...opts,
+        installStyleIndex: opts.baseStyle,
       })
 
       await loadEnvFiles(options.cwd)
@@ -228,8 +229,8 @@ export const init = new Command()
             // Store config to be merged into components.json later.
             options.registryBaseConfig = item.config
           }
-          options.baseStyle =
-            item.extends === "none" ? false : options.baseStyle
+          options.installStyleIndex =
+            item.extends === "none" ? false : options.installStyleIndex
         }
 
         if (item?.type === "registry:style") {
@@ -238,14 +239,13 @@ export const init = new Command()
           options.baseColor = "neutral"
 
           // If the style extends none, we don't want to install the base style.
-          options.baseStyle =
-            item.extends === "none" ? false : options.baseStyle
+          options.installStyleIndex =
+            item.extends === "none" ? false : options.installStyleIndex
         }
       }
 
       // If --no-base-style, we don't want to prompt for a base color either.
-      // The style will extend or override it.
-      if (!options.baseStyle) {
+      if (!options.installStyleIndex) {
         options.baseColor = "neutral"
       }
 
@@ -326,7 +326,7 @@ export async function runInit(
     // Why index? Because when style is true, we read style from components.json and fetch that.
     // i.e new-york from components.json then fetch /styles/new-york/index.
     // TODO: Fix this so that we can extend any style i.e --style=new-york.
-    ...(options.baseStyle ? ["index"] : []),
+    ...(options.installStyleIndex ? ["index"] : []),
     ...(options.components ?? []),
   ]
 
@@ -389,7 +389,6 @@ export async function runInit(
     // Init will always overwrite files.
     overwrite: true,
     silent: options.silent,
-    baseStyle: options.baseStyle,
     isNewProject:
       options.isNewProject || projectInfo?.framework.name === "next-app",
   })
diff --git a/packages/shadcn/src/utils/add-components.ts b/packages/shadcn/src/utils/add-components.ts
index 3b6a4bac2d..38663a04a3 100644
--- a/packages/shadcn/src/utils/add-components.ts
+++ b/packages/shadcn/src/utils/add-components.ts
@@ -38,7 +38,6 @@ export async function addComponents(
     overwrite?: boolean
     silent?: boolean
     isNewProject?: boolean
-    baseStyle?: boolean
     registryHeaders?: Record<string, Record<string, string>>
     path?: string
   }
@@ -47,7 +46,6 @@ export async function addComponents(
     overwrite: false,
     silent: false,
     isNewProject: false,
-    baseStyle: true,
     ...options,
   }
 
@@ -74,11 +72,10 @@ async function addProjectComponents(
     overwrite?: boolean
     silent?: boolean
     isNewProject?: boolean
-    baseStyle?: boolean
     path?: string
   }
 ) {
-  if (!options.baseStyle && !components.length) {
+  if (!components.length) {
     return
   }
 
@@ -117,7 +114,6 @@ async function addProjectComponents(
     tailwindVersion,
     tailwindConfig: tree.tailwind?.config,
     overwriteCssVars,
-    initIndex: options.baseStyle,
   })
 
   // Add CSS updater
@@ -157,11 +153,10 @@ async function addWorkspaceComponents(
     silent?: boolean
     isNewProject?: boolean
     isRemote?: boolean
-    baseStyle?: boolean
     path?: string
   }
 ) {
-  if (!options.baseStyle && !components.length) {
+  if (!components.length) {
     return
   }
 
diff --git a/packages/shadcn/src/utils/updaters/update-css-vars.ts b/packages/shadcn/src/utils/updaters/update-css-vars.ts
index f14af41638..fc1aea4109 100644
--- a/packages/shadcn/src/utils/updaters/update-css-vars.ts
+++ b/packages/shadcn/src/utils/updaters/update-css-vars.ts
@@ -5,7 +5,6 @@ import {
   registryItemTailwindSchema,
 } from "@/src/schema"
 import { Config } from "@/src/utils/get-config"
-import { getPackageInfo } from "@/src/utils/get-package-info"
 import { TailwindVersion } from "@/src/utils/get-project-info"
 import { highlighter } from "@/src/utils/highlighter"
 import { spinner } from "@/src/utils/spinner"
@@ -21,7 +20,6 @@ export async function updateCssVars(
   options: {
     cleanupDefaultNextStyles?: boolean
     overwriteCssVars?: boolean
-    initIndex?: boolean
     silent?: boolean
     tailwindVersion?: TailwindVersion
     tailwindConfig?: z.infer<typeof registryItemTailwindSchema>["config"]
@@ -36,7 +34,6 @@ export async function updateCssVars(
     silent: false,
     tailwindVersion: "v3",
     overwriteCssVars: false,
-    initIndex: true,
     ...options,
   }
   const cssFilepath = config.resolvedPaths.tailwindCss
@@ -56,7 +53,6 @@ export async function updateCssVars(
     tailwindVersion: options.tailwindVersion,
     tailwindConfig: options.tailwindConfig,
     overwriteCssVars: options.overwriteCssVars,
-    initIndex: options.initIndex,
   })
   await fs.writeFile(cssFilepath, output, "utf8")
   cssVarsSpinner.succeed()
@@ -71,13 +67,11 @@ export async function transformCssVars(
     tailwindVersion?: TailwindVersion
     tailwindConfig?: z.infer<typeof registryItemTailwindSchema>["config"]
     overwriteCssVars?: boolean
-    initIndex?: boolean
   } = {
     cleanupDefaultNextStyles: false,
     tailwindVersion: "v3",
     tailwindConfig: undefined,
     overwriteCssVars: false,
-    initIndex: false,
   }
 ) {
   options = {
@@ -85,7 +79,6 @@ export async function transformCssVars(
     tailwindVersion: "v3",
     tailwindConfig: undefined,
     overwriteCssVars: false,
-    initIndex: false,
     ...options,
   }
 
@@ -98,18 +91,6 @@ export async function transformCssVars(
   if (options.tailwindVersion === "v4") {
     plugins = []
 
-    // Only add tw-animate-css if project does not have tailwindcss-animate
-    if (config.resolvedPaths?.cwd) {
-      const packageInfo = getPackageInfo(config.resolvedPaths.cwd)
-      if (
-        !packageInfo?.dependencies?.["tailwindcss-animate"] &&
-        !packageInfo?.devDependencies?.["tailwindcss-animate"] &&
-        options.initIndex
-      ) {
-        plugins.push(addCustomImport({ params: "tw-animate-css" }))
-      }
-    }
-
     plugins.push(addCustomVariant({ params: "dark (&:is(.dark *))" }))
 
     if (options.cleanupDefaultNextStyles) {
@@ -130,12 +111,6 @@ export async function transformCssVars(
     }
   }
 
-  if (config.tailwind.cssVariables && options.initIndex) {
-    plugins.push(
-      updateBaseLayerPlugin({ tailwindVersion: options.tailwindVersion })
-    )
-  }
-
   const result = await postcss(plugins).process(input, {
     from: undefined,
   })
@@ -151,81 +126,6 @@ export async function transformCssVars(
   return output
 }
 
-function updateBaseLayerPlugin({
-  tailwindVersion,
-}: {
-  tailwindVersion?: TailwindVersion
-}) {
-  return {
-    postcssPlugin: "update-base-layer",
-    Once(root: Root) {
-      const requiredRules = [
-        {
-          selector: "*",
-          apply:
-            tailwindVersion === "v4"
-              ? "border-border outline-ring/50"
-              : "border-border",
-        },
-        { selector: "body", apply: "bg-background text-foreground" },
-      ]
-
-      let baseLayer = root.nodes.find(
-        (node): node is AtRule =>
-          node.type === "atrule" &&
-          node.name === "layer" &&
-          node.params === "base" &&
-          requiredRules.every(({ selector, apply }) =>
-            node.nodes?.some(
-              (rule): rule is Rule =>
-                rule.type === "rule" &&
-                rule.selector === selector &&
-                rule.nodes.some(
-                  (applyRule): applyRule is AtRule =>
-                    applyRule.type === "atrule" &&
-                    applyRule.name === "apply" &&
-                    applyRule.params === apply
-                )
-            )
-          )
-      ) as AtRule | undefined
-
-      if (!baseLayer) {
-        baseLayer = postcss.atRule({
-          name: "layer",
-          params: "base",
-          raws: { semicolon: true, between: " ", before: "\n" },
-        })
-        root.append(baseLayer)
-        root.insertBefore(baseLayer, postcss.comment({ text: "---break---" }))
-      }
-
-      requiredRules.forEach(({ selector, apply }) => {
-        const existingRule = baseLayer?.nodes?.find(
-          (node): node is Rule =>
-            node.type === "rule" && node.selector === selector
-        )
-
-        if (!existingRule) {
-          baseLayer?.append(
-            postcss.rule({
-              selector,
-              nodes: [
-                postcss.atRule({
-                  name: "apply",
-                  params: apply,
-                  raws: { semicolon: true, before: "\n    " },
-                }),
-              ],
-              raws: { semicolon: true, between: " ", before: "\n  " },
-            })
-          )
-        }
-      })
-    },
-  }
-}
-
 function updateCssVarsPlugin(
   cssVars: z.infer<typeof registryItemCssVarsSchema>
 ) {
@@ -662,13 +562,13 @@ function addCustomImport({ params }: { params: string }) {
           node.type === "atrule" && node.name === "import"
       )
 
-      // Find custom variant node (to ensure we insert before it)
+      // Find custom variant node (to ensure we insert before it).
       const customVariantNode = root.nodes.find(
         (node): node is AtRule =>
           node.type === "atrule" && node.name === "custom-variant"
       )
 
-      // Check if our specific import already exists
+      // Check if our specific import already exists.
       const hasImport = importNodes.some(
         (node) => node.params.replace(/["']/g, "") === params
       )
@@ -681,18 +581,18 @@ function addCustomImport({ params }: { params: string }) {
         })
 
         if (importNodes.length > 0) {
-          // If there are existing imports, add after the last import
+          // If there are existing imports, add after the last import.
           const lastImport = importNodes[importNodes.length - 1]
           root.insertAfter(lastImport, importNode)
         } else if (customVariantNode) {
-          // If no imports but has custom-variant, insert before it
+          // If no imports but has custom-variant, insert before it.
           root.insertBefore(customVariantNode, importNode)
           root.insertBefore(
             customVariantNode,
             postcss.comment({ text: "---break---" })
           )
         } else {
-          // If no imports and no custom-variant, insert at the start
+          // If no imports and no custom-variant, insert at the start.
           root.prepend(importNode)
           root.insertAfter(importNode, postcss.comment({ text: "---break---" }))
         }
diff --git a/packages/shadcn/src/utils/updaters/update-css.ts b/packages/shadcn/src/utils/updaters/update-css.ts
index 13b2c74357..37243225f5 100644
--- a/packages/shadcn/src/utils/updaters/update-css.ts
+++ b/packages/shadcn/src/utils/updaters/update-css.ts
@@ -472,12 +472,23 @@ function processRule(parent: Root | AtRule, selector: string, properties: any) {
         const atRuleMatch = prop.match(/@([a-zA-Z-]+)\s*(.*)/)
         if (atRuleMatch) {
           const [, atRuleName, atRuleParams] = atRuleMatch
-          const atRule = postcss.atRule({
-            name: atRuleName,
-            params: atRuleParams,
-            raws: { semicolon: true, before: "\n    " },
-          })
-          rule.append(atRule)
+
+          // Check if this at-rule already exists in the rule.
+          const existingAtRule = rule.nodes?.find(
+            (node): node is AtRule =>
+              node.type === "atrule" &&
+              node.name === atRuleName &&
+              node.params === atRuleParams
+          )
+
+          if (!existingAtRule) {
+            const atRule = postcss.atRule({
+              name: atRuleName,
+              params: atRuleParams,
+              raws: { semicolon: true, before: "\n    " },
+            })
+            rule.append(atRule)
+          }
         }
       } else if (typeof value === "string") {
         const decl = postcss.decl({
diff --git a/packages/shadcn/test/utils/updaters/update-css.test.ts b/packages/shadcn/test/utils/updaters/update-css.test.ts
index c1d3a6fb5f..3470409922 100644
--- a/packages/shadcn/test/utils/updaters/update-css.test.ts
+++ b/packages/shadcn/test/utils/updaters/update-css.test.ts
@@ -853,6 +853,82 @@ describe("transformCss", () => {
     `)
   })
 
+  test("should add base layer styles from registry:style css field", async () => {
+    const input = `@import "tailwindcss";`
+
+    // This is the exact shape from the registry:style index item.
+    const result = await transformCss(input, {
+      '@import "tw-animate-css"': {},
+      '@import "shadcn/tailwind.css"': {},
+      "@layer base": {
+        "*": {
+          "@apply border-border outline-ring/50": {},
+        },
+        body: {
+          "@apply bg-background text-foreground": {},
+        },
+      },
+    })
+
+    expect(result).toMatchInlineSnapshot(`
+      "@import "tailwindcss";
+      @import "tw-animate-css";
+      @import "shadcn/tailwind.css";
+
+      @layer base {
+        * {
+          @apply border-border outline-ring/50;
+        }
+        body {
+          @apply bg-background text-foreground;
+        }
+      }"
+    `)
+  })
+
+  test("should not duplicate base layer styles if already present", async () => {
+    const input = `@import "tailwindcss";
+@import "tw-animate-css";
+@import "shadcn/tailwind.css";
+
+@layer base {
+  * {
+    @apply border-border outline-ring/50;
+  }
+  body {
+    @apply bg-background text-foreground;
+  }
+}`
+
+    const result = await transformCss(input, {
+      '@import "tw-animate-css"': {},
+      '@import "shadcn/tailwind.css"': {},
+      "@layer base": {
+        "*": {
+          "@apply border-border outline-ring/50": {},
+        },
+        body: {
+          "@apply bg-background text-foreground": {},
+        },
+      },
+    })
+
+    expect(result).toMatchInlineSnapshot(`
+      "@import "tailwindcss";
+      @import "tw-animate-css";
+      @import "shadcn/tailwind.css";
+
+      @layer base {
+        * {
+          @apply border-border outline-ring/50;
+        }
+        body {
+          @apply bg-background text-foreground;
+        }
+      }"
+    `)
+  })
+
   test("should replace existing keyframes instead of duplicating", async () => {
     const input = `@import "tailwindcss";