diff --git a/.ci/lint-all.sh b/.ci/lint-all.sh
index 671ea3365d99..91833f705e48 100755
--- a/.ci/lint-all.sh
+++ b/.ci/lint-all.sh
@@ -8,7 +8,6 @@ pwsh -file ./.ci/lint-powershell.ps1 || exit 1
 
 conda create -q -y -n test-env \
     "python=3.13[build=*_cp*]" \
-    'biome>=1.9.3' \
     'pre-commit>=3.8.0' \
     'r-lintr>=3.1.2'
 
@@ -20,6 +19,3 @@ pre-commit run --all-files || exit 1
 
 echo "Linting R code"
 Rscript ./.ci/lint-r-code.R "$(pwd)" || exit 1
-
-echo "Linting JavaScript code"
-bash ./.ci/lint-js.sh || exit 1
diff --git a/.ci/lint-js.sh b/.ci/lint-js.sh
deleted file mode 100644
index 534f251620e2..000000000000
--- a/.ci/lint-js.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-set -e -E -u -o pipefail
-
-biome ci --config-path=./biome.json --diagnostic-level=info --error-on-warnings ./
diff --git a/.gitignore b/.gitignore
index f3a386af25ad..d8c7191d07cc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -313,6 +313,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
@@ -320,8 +321,11 @@ nosetests.xml
 prof/
 *.prof
 coverage.xml
-*,cover
+*.cover
+*.py.cover
 .hypothesis/
+.pytest_cache/
+cover/
 **/coverage.html
 **/coverage.html.zip
 **/Rplots.pdf
@@ -469,3 +473,8 @@ dask-worker-space/
 
 # pixi environments
 .pixi
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fcb0c711049e..2e15f4b3954d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -62,17 +62,22 @@ repos:
           - sphinx>=8.1.3
           - sphinx_rtd_theme>=3.0.1
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
     rev: v0.14.0
     hooks:
-      # Run the linter.
       - id: ruff-check
         args: ["--config", "python-package/pyproject.toml"]
         types_or: [python, jupyter]
-      # Run the formatter.
       - id: ruff-format
         args: ["--config", "python-package/pyproject.toml"]
         types_or: [python, jupyter]
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.2.5
+    hooks:
+      - id: biome-ci
+        args:
+          - --config-path=./biome.json
+          - --diagnostic-level=info
+          - --error-on-warnings
   - repo: https://github.com/shellcheck-py/shellcheck-py
     rev: v0.10.0.1
     hooks:
diff --git a/biome.json b/biome.json
index 95995e7e13b7..0d163adebcbf 100644
--- a/biome.json
+++ b/biome.json
@@ -1,21 +1,28 @@
 {
-    "files": {
-        "ignore": [".mypy_cache/", ".pixi/"]
+    "root": false,
+    "vcs": {
+        "enabled": true,
+        "clientKind": "git",
+        "useIgnoreFile": true
     },
     "formatter": {
         "enabled": true,
-        "useEditorconfig": true
+        "useEditorconfig": true,
+        "lineWidth": 120
     },
-    "organizeImports": {
-        "enabled": true
+    "assist": {
+        "enabled": true,
+        "actions": {
+            "recommended": true
+        }
     },
     "linter": {
         "enabled": true,
+        "domains": {
+            "project": "all"
+        },
         "rules": {
-            "all": true
+            "recommended": true
         }
-    },
-    "javascript": {
-        "globals": ["$"]
     }
 }