diff --git a/deps/cli/package.json b/deps/cli/package.json
index 05615b9ca0..02e538a979 100644
--- a/deps/cli/package.json
+++ b/deps/cli/package.json
@@ -12,7 +12,7 @@
   "dependencies": {
     "@logseq/nbb-logseq": "github:logseq/nbb-logseq#feat-db-v31",
     "@modelcontextprotocol/sdk": "^1.17.5",
-    "better-sqlite3": "~11.10.0",
+    "better-sqlite3": "^12.6.2",
     "fastify": "5.3.2",
     "fs-extra": "^11.3.0",
     "jszip": "3.8.0",
diff --git a/deps/cli/yarn.lock b/deps/cli/yarn.lock
index 30fe2bf9ed..5c0804f58f 100644
--- a/deps/cli/yarn.lock
+++ b/deps/cli/yarn.lock
@@ -135,10 +135,10 @@ base64-js@^1.3.1:
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
 
-better-sqlite3@~11.10.0:
-  version "11.10.0"
-  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-11.10.0.tgz#2b1b14c5acd75a43fd84d12cc291ea98cef57d98"
-  integrity sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==
+better-sqlite3@^12.6.2:
+  version "12.6.2"
+  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-12.6.2.tgz#770649f28a62e543a360f3dfa1afe4cc944b1937"
+  integrity sha512-8VYKM3MjCa9WcaSAI3hzwhmyHVlH8tiGFwf0RlTsZPWJ1I5MkzjiudCo4KC4DxOaL/53A5B1sI/IbldNFDbsKA==
   dependencies:
     bindings "^1.5.0"
     prebuild-install "^7.1.1"
diff --git a/deps/db/package.json b/deps/db/package.json
index 2683b101a3..be569ce802 100644
--- a/deps/db/package.json
+++ b/deps/db/package.json
@@ -7,7 +7,7 @@
     "fs-extra": "^11.3.0"
   },
   "dependencies": {
-    "better-sqlite3": "11.10.0"
+    "better-sqlite3": "^12.6.2"
   },
   "scripts": {
     "test": "yarn nbb-logseq -cp test -m nextjournal.test-runner",
diff --git a/deps/db/yarn.lock b/deps/db/yarn.lock
index 9a5698efd3..7d62d83877 100644
--- a/deps/db/yarn.lock
+++ b/deps/db/yarn.lock
@@ -13,10 +13,10 @@ base64-js@^1.3.1:
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
 
-better-sqlite3@11.10.0:
-  version "11.10.0"
-  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-11.10.0.tgz#2b1b14c5acd75a43fd84d12cc291ea98cef57d98"
-  integrity sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==
+better-sqlite3@^12.6.2:
+  version "12.6.2"
+  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-12.6.2.tgz#770649f28a62e543a360f3dfa1afe4cc944b1937"
+  integrity sha512-8VYKM3MjCa9WcaSAI3hzwhmyHVlH8tiGFwf0RlTsZPWJ1I5MkzjiudCo4KC4DxOaL/53A5B1sI/IbldNFDbsKA==
   dependencies:
     bindings "^1.5.0"
     prebuild-install "^7.1.1"
diff --git a/deps/graph-parser/package.json b/deps/graph-parser/package.json
index 95e91d2934..84490888a0 100644
--- a/deps/graph-parser/package.json
+++ b/deps/graph-parser/package.json
@@ -4,7 +4,7 @@
   "private": true,
   "devDependencies": {
     "@logseq/nbb-logseq": "github:logseq/nbb-logseq#feat-db-v31",
-    "better-sqlite3": "11.10.0"
+    "better-sqlite3": "^12.6.2"
   },
   "dependencies": {
     "mldoc": "^1.5.9",
diff --git a/deps/graph-parser/yarn.lock b/deps/graph-parser/yarn.lock
index a21ee96d23..12e248e8c7 100644
--- a/deps/graph-parser/yarn.lock
+++ b/deps/graph-parser/yarn.lock
@@ -23,10 +23,10 @@ base64-js@^1.3.1:
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
 
-better-sqlite3@11.10.0:
-  version "11.10.0"
-  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-11.10.0.tgz#2b1b14c5acd75a43fd84d12cc291ea98cef57d98"
-  integrity sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==
+better-sqlite3@^12.6.2:
+  version "12.6.2"
+  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-12.6.2.tgz#770649f28a62e543a360f3dfa1afe4cc944b1937"
+  integrity sha512-8VYKM3MjCa9WcaSAI3hzwhmyHVlH8tiGFwf0RlTsZPWJ1I5MkzjiudCo4KC4DxOaL/53A5B1sI/IbldNFDbsKA==
   dependencies:
     bindings "^1.5.0"
     prebuild-install "^7.1.1"
diff --git a/deps/outliner/package.json b/deps/outliner/package.json
index 3b468a0ed1..10836e94b2 100644
--- a/deps/outliner/package.json
+++ b/deps/outliner/package.json
@@ -6,7 +6,7 @@
     "@logseq/nbb-logseq": "github:logseq/nbb-logseq#feat-db-v31"
   },
   "dependencies": {
-    "better-sqlite3": "11.10.0",
+    "better-sqlite3": "^12.6.2",
     "mldoc": "^1.5.9"
   },
   "scripts": {
diff --git a/deps/outliner/yarn.lock b/deps/outliner/yarn.lock
index 3fff63e2e8..4319d64e7e 100644
--- a/deps/outliner/yarn.lock
+++ b/deps/outliner/yarn.lock
@@ -23,10 +23,10 @@ base64-js@^1.3.1:
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
 
-better-sqlite3@11.10.0:
-  version "11.10.0"
-  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-11.10.0.tgz#2b1b14c5acd75a43fd84d12cc291ea98cef57d98"
-  integrity sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==
+better-sqlite3@^12.6.2:
+  version "12.6.2"
+  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-12.6.2.tgz#770649f28a62e543a360f3dfa1afe4cc944b1937"
+  integrity sha512-8VYKM3MjCa9WcaSAI3hzwhmyHVlH8tiGFwf0RlTsZPWJ1I5MkzjiudCo4KC4DxOaL/53A5B1sI/IbldNFDbsKA==
   dependencies:
     bindings "^1.5.0"
     prebuild-install "^7.1.1"
diff --git a/deps/publishing/package.json b/deps/publishing/package.json
index 4690c436a1..6d2ab77eea 100644
--- a/deps/publishing/package.json
+++ b/deps/publishing/package.json
@@ -7,7 +7,7 @@
     "mldoc": "^1.5.9"
   },
   "dependencies": {
-    "better-sqlite3": "11.10.0",
+    "better-sqlite3": "^12.6.2",
     "fs-extra": "9.1.0"
   },
   "scripts": {
diff --git a/deps/publishing/yarn.lock b/deps/publishing/yarn.lock
index 9ac029e25f..680bf984f8 100644
--- a/deps/publishing/yarn.lock
+++ b/deps/publishing/yarn.lock
@@ -28,10 +28,10 @@ base64-js@^1.3.1:
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
 
-better-sqlite3@11.10.0:
-  version "11.10.0"
-  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-11.10.0.tgz#2b1b14c5acd75a43fd84d12cc291ea98cef57d98"
-  integrity sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==
+better-sqlite3@^12.6.2:
+  version "12.6.2"
+  resolved "https://registry.yarnpkg.com/better-sqlite3/-/better-sqlite3-12.6.2.tgz#770649f28a62e543a360f3dfa1afe4cc944b1937"
+  integrity sha512-8VYKM3MjCa9WcaSAI3hzwhmyHVlH8tiGFwf0RlTsZPWJ1I5MkzjiudCo4KC4DxOaL/53A5B1sI/IbldNFDbsKA==
   dependencies:
     bindings "^1.5.0"
     prebuild-install "^7.1.1"