diff --git a/.changeset/fast-pianos-teach.md b/.changeset/fast-pianos-teach.md
new file mode 100644
index 000000000..6b95b97cc
--- /dev/null
+++ b/.changeset/fast-pianos-teach.md
@@ -0,0 +1,6 @@
+---
+"@tanstack/browser-db-sqlite-persistence": patch
+"@tanstack/db-sqlite-persistence-core": patch
+---
+
+Fix SQLite expression-index matching for persisted ref filters by inlining JSON-path literals in runtime SQL compilation while keeping actual filter values bound.
diff --git a/packages/db-sqlite-persistence-core/src/sqlite-core-adapter.ts b/packages/db-sqlite-persistence-core/src/sqlite-core-adapter.ts
index 6bbf06c4d..53a093c8e 100644
--- a/packages/db-sqlite-persistence-core/src/sqlite-core-adapter.ts
+++ b/packages/db-sqlite-persistence-core/src/sqlite-core-adapter.ts
@@ -579,18 +579,21 @@ function compileComparisonSql(
 function compileRefExpressionSql(jsonPath: string): CompiledSqlFragment {
   const typePath = `${jsonPath}.${PERSISTED_TYPE_TAG}`
   const taggedValuePath = `${jsonPath}.${PERSISTED_VALUE_TAG}`
+  const typePathSql = toSqliteLiteral(typePath)
+  const taggedValuePathSql = toSqliteLiteral(taggedValuePath)
+  const jsonPathSql = toSqliteLiteral(jsonPath)
 
   return {
     supported: true,
-    sql: `(CASE json_extract(value, ?)
-      WHEN 'bigint' THEN CAST(json_extract(value, ?) AS NUMERIC)
-      WHEN 'date' THEN json_extract(value, ?)
+    sql: `(CASE json_extract(value, ${typePathSql})
+      WHEN 'bigint' THEN CAST(json_extract(value, ${taggedValuePathSql}) AS NUMERIC)
+      WHEN 'date' THEN json_extract(value, ${taggedValuePathSql})
       WHEN 'nan' THEN NULL
       WHEN 'infinity' THEN NULL
       WHEN '-infinity' THEN NULL
-      ELSE json_extract(value, ?)
+      ELSE json_extract(value, ${jsonPathSql})
     END)`,
-    params: [typePath, taggedValuePath, taggedValuePath, jsonPath],
+    params: [],
     valueKind: `unknown`,
   }
 }
diff --git a/packages/db-sqlite-persistence-core/tests/sqlite-core-adapter.test.ts b/packages/db-sqlite-persistence-core/tests/sqlite-core-adapter.test.ts
index d02f2a635..7a6cddbc5 100644
--- a/packages/db-sqlite-persistence-core/tests/sqlite-core-adapter.test.ts
+++ b/packages/db-sqlite-persistence-core/tests/sqlite-core-adapter.test.ts
@@ -230,6 +230,36 @@ function registerHarness(
   return harness
 }
 
+function createQueryObservingDriver(
+  inner: SQLiteDriver,
+  observeQuery: (
+    sql: string,
+    params: ReadonlyArray<unknown>,
+  ) => void | Promise<void>,
+): SQLiteDriver {
+  const wrap = (driver: SQLiteDriver): SQLiteDriver => {
+    const transactionWithDriver = driver.transactionWithDriver
+
+    return {
+      exec: async (sql) => driver.exec(sql),
+      query: async <T>(sql: string, params?: ReadonlyArray<unknown>) => {
+        await observeQuery(sql, params ?? [])
+        return driver.query<T>(sql, params)
+      },
+      run: async (sql, params) => driver.run(sql, params),
+      transaction: async <T>(
+        fn: (transactionDriver: SQLiteDriver) => Promise<T>,
+      ) => driver.transaction((transactionDriver) => fn(wrap(transactionDriver))),
+      transactionWithDriver: transactionWithDriver
+        ? async <T>(fn: (transactionDriver: SQLiteDriver) => Promise<T>) =>
+            transactionWithDriver((transactionDriver) => fn(wrap(transactionDriver)))
+        : undefined,
+    }
+  }
+
+  return wrap(inner)
+}
+
 export type SQLiteCoreAdapterHarnessFactory = (
   options?: Omit<
     ConstructorParameters<typeof SQLiteCorePersistenceAdapter>[0],
@@ -1609,6 +1639,94 @@ export function runSQLiteCoreAdapterContractSuite(
       )
     })
 
+    it(`inlines JSON-path refs in runtime subset filters while keeping values bound`, async () => {
+      const baseHarness = registerHarness()
+      const collectionId = `thread-messages`
+      let capturedSubsetSql: string | undefined
+      let capturedSubsetParams: ReadonlyArray<unknown> = []
+
+      const driver = createQueryObservingDriver(
+        baseHarness.driver,
+        (sql, params) => {
+          if (
+            sql.startsWith(`SELECT key, value, metadata, row_version FROM`) &&
+            sql.includes(`WHERE`)
+          ) {
+            capturedSubsetSql = sql
+            capturedSubsetParams = params
+          }
+        },
+      )
+      const adapter = new SQLiteCorePersistenceAdapter({ driver })
+
+      await adapter.applyCommittedTx(collectionId, {
+        txId: `thread-messages-seed`,
+        term: 1,
+        seq: 1,
+        rowVersion: 1,
+        mutations: [
+          {
+            type: `insert`,
+            key: `1`,
+            value: {
+              id: `1`,
+              threadId: `thread-1`,
+              title: `First`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 1,
+            },
+          },
+          {
+            type: `insert`,
+            key: `2`,
+            value: {
+              id: `2`,
+              threadId: `thread-1`,
+              title: `Second`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 2,
+            },
+          },
+          {
+            type: `insert`,
+            key: `3`,
+            value: {
+              id: `3`,
+              threadId: `thread-2`,
+              title: `Other thread`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 3,
+            },
+          },
+        ],
+      })
+
+      await adapter.ensureIndex(collectionId, `thread-id`, {
+        expressionSql: [
+          JSON.stringify({
+            type: `ref`,
+            path: [`threadId`],
+          }),
+        ],
+      })
+
+      const rows = await adapter.loadSubset(collectionId, {
+        where: new IR.Func(`eq`, [
+          new IR.PropRef([`threadId`]),
+          new IR.Value(`thread-1`),
+        ]),
+      })
+
+      expect(rows).toHaveLength(2)
+      expect(rows.map((row) => String(row.key)).sort()).toEqual([`1`, `2`])
+      expect(capturedSubsetSql).toContain(`WHERE`)
+      expect(capturedSubsetSql).toContain(
+        `json_extract(value, '$.threadId.__tanstack_db_persisted_type__')`,
+      )
+      expect(capturedSubsetSql).toContain(`json_extract(value, '$.threadId')`)
+      expect(capturedSubsetParams).toEqual([`thread-1`])
+    })
+
     it(`rejects unsafe raw SQL fragments in index specs`, async () => {
       const { adapter } = registerContractHarness()
 
diff --git a/packages/node-db-sqlite-persistence/tests/node-sqlite-core-adapter-contract.test.ts b/packages/node-db-sqlite-persistence/tests/node-sqlite-core-adapter-contract.test.ts
index 55b41e20e..cff65b1ce 100644
--- a/packages/node-db-sqlite-persistence/tests/node-sqlite-core-adapter-contract.test.ts
+++ b/packages/node-db-sqlite-persistence/tests/node-sqlite-core-adapter-contract.test.ts
@@ -1,10 +1,16 @@
 import { mkdtempSync, rmSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
+import { describe, expect, it } from 'vitest'
+import { IR } from '@tanstack/db'
 import { runSQLiteCoreAdapterContractSuite } from '../../db-sqlite-persistence-core/tests/contracts/sqlite-core-adapter-contract'
 import { BetterSqlite3SQLiteDriver } from '../src/node-driver'
-import { SQLiteCorePersistenceAdapter } from '../../db-sqlite-persistence-core/src'
+import {
+  SQLiteCorePersistenceAdapter,
+  createPersistedTableName,
+} from '../../db-sqlite-persistence-core/src'
 import type { SQLiteCoreAdapterHarnessFactory } from '../../db-sqlite-persistence-core/tests/contracts/sqlite-core-adapter-contract'
+import type { SQLiteDriver } from '../../db-sqlite-persistence-core/src'
 
 const createHarness: SQLiteCoreAdapterHarnessFactory = (options) => {
   const tempDirectory = mkdtempSync(join(tmpdir(), `db-node-sqlite-core-`))
@@ -32,3 +38,155 @@ runSQLiteCoreAdapterContractSuite(
   `SQLiteCorePersistenceAdapter (better-sqlite3 node driver)`,
   createHarness,
 )
+
+function createQueryObservingDriver(
+  inner: SQLiteDriver,
+  observeQuery: (
+    sql: string,
+    params: ReadonlyArray<unknown>,
+  ) => void | Promise<void>,
+): SQLiteDriver {
+  const wrap = (driver: SQLiteDriver): SQLiteDriver => {
+    return {
+      exec: async function (sql) {
+        return driver.exec(sql)
+      },
+      query: async function <T>(
+        sql: string,
+        params?: ReadonlyArray<unknown>,
+      ) {
+        await observeQuery(sql, params ?? [])
+        return driver.query<T>(sql, params)
+      },
+      run: async function (sql, params) {
+        return driver.run(sql, params)
+      },
+      transaction: async function <T>(
+        fn: (transactionDriver: SQLiteDriver) => Promise<T>,
+      ) {
+        return driver.transaction((transactionDriver) =>
+          fn(wrap(transactionDriver)),
+        )
+      },
+      transactionWithDriver: driver.transactionWithDriver
+        ? async function <T>(
+            fn: (transactionDriver: SQLiteDriver) => Promise<T>,
+          ) {
+            return driver.transactionWithDriver!((
+              transactionDriver,
+            ) =>
+              fn(wrap(transactionDriver)),
+            )
+          }
+        : undefined,
+    }
+  }
+
+  return wrap(inner)
+}
+
+describe(`SQLiteCorePersistenceAdapter planner behavior (better-sqlite3)`, () => {
+  it(`uses expression indexes for runtime ref filters`, async () => {
+    const tempDirectory = mkdtempSync(join(tmpdir(), `db-node-sqlite-plan-`))
+    const dbPath = join(tempDirectory, `state.sqlite`)
+    const baseDriver = new BetterSqlite3SQLiteDriver({ filename: dbPath })
+    const collectionId = `thread-messages`
+    const tableName = createPersistedTableName(collectionId, `c`)
+    let capturedSubsetSql: string | undefined
+    let capturedSubsetParams: ReadonlyArray<unknown> = []
+
+    const driver = createQueryObservingDriver(baseDriver, (sql, params) => {
+      if (
+        sql.startsWith(`SELECT key, value, metadata, row_version FROM`) &&
+        sql.includes(`WHERE`)
+      ) {
+        capturedSubsetSql = sql
+        capturedSubsetParams = params
+      }
+    })
+    const adapter = new SQLiteCorePersistenceAdapter({ driver })
+
+    try {
+      await adapter.applyCommittedTx(collectionId, {
+        txId: `thread-messages-seed`,
+        term: 1,
+        seq: 1,
+        rowVersion: 1,
+        mutations: [
+          {
+            type: `insert`,
+            key: `1`,
+            value: {
+              id: `1`,
+              threadId: `thread-1`,
+              title: `First`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 1,
+            },
+          },
+          {
+            type: `insert`,
+            key: `2`,
+            value: {
+              id: `2`,
+              threadId: `thread-1`,
+              title: `Second`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 2,
+            },
+          },
+          {
+            type: `insert`,
+            key: `3`,
+            value: {
+              id: `3`,
+              threadId: `thread-2`,
+              title: `Other thread`,
+              createdAt: `2026-01-01T00:00:00.000Z`,
+              score: 3,
+            },
+          },
+        ],
+      })
+
+      await adapter.ensureIndex(collectionId, `thread-id`, {
+        expressionSql: [
+          JSON.stringify({
+            type: `ref`,
+            path: [`threadId`],
+          }),
+        ],
+      })
+
+      const rows = await adapter.loadSubset(collectionId, {
+        where: new IR.Func(`eq`, [
+          new IR.PropRef([`threadId`]),
+          new IR.Value(`thread-1`),
+        ]),
+      })
+
+      expect(rows).toHaveLength(2)
+      expect(capturedSubsetSql).toContain(`WHERE`)
+      expect(capturedSubsetParams).toEqual([`thread-1`])
+
+      const planRows = baseDriver
+        .getDatabase()
+        .prepare(`EXPLAIN QUERY PLAN ${capturedSubsetSql}`)
+        .all(...capturedSubsetParams) as Array<{ detail: string }>
+      const indexedSearchPattern = new RegExp(
+        `\\bSEARCH ${tableName}\\b.*\\bUSING INDEX\\b`,
+      )
+
+      expect(planRows.map((row) => row.detail).length).toBeGreaterThan(0)
+      expect(
+        planRows.some((row) => indexedSearchPattern.test(row.detail)),
+      ).toBe(true)
+      expect(
+        planRows.some((row) => row.detail.startsWith(`SCAN ${tableName}`)),
+      ).toBe(false)
+    } finally {
+      baseDriver.close()
+      rmSync(tempDirectory, { recursive: true, force: true })
+    }
+  })
+})