diff --git a/packages/router-plugin/src/core/config.ts b/packages/router-plugin/src/core/config.ts
index d776c7cd5b..f93166d392 100644
--- a/packages/router-plugin/src/core/config.ts
+++ b/packages/router-plugin/src/core/config.ts
@@ -105,7 +105,7 @@ export const configSchema = generatorConfigSchema.extend({
 export const getConfig = (inlineConfig: Partial<Config>, root: string) => {
   const config = getGeneratorConfig(inlineConfig, root)
 
-  return configSchema.parse({ ...config, ...inlineConfig })
+  return configSchema.parse({ ...inlineConfig, ...config })
 }
 
 export type Config = z.infer<typeof configSchema>
diff --git a/packages/router-plugin/tests/config.test.ts b/packages/router-plugin/tests/config.test.ts
new file mode 100644
index 0000000000..2f3e8cc7db
--- /dev/null
+++ b/packages/router-plugin/tests/config.test.ts
@@ -0,0 +1,112 @@
+import path from 'node:path'
+import { readFileSync } from 'node:fs'
+import { describe, expect, it } from 'vitest'
+import { getConfig } from '../src'
+import type { Config } from '../src'
+
+describe('getConfig', () => {
+  const testCases = [
+    {
+      name: 'inline config',
+      inlineConfig: {
+        target: 'solid',
+        autoCodeSplitting: false,
+        enableRouteGeneration: true,
+      } as Partial<Config>,
+      withJson: false,
+    },
+    {
+      name: `inline config and relative paths`,
+      inlineConfig: {
+        target: 'solid',
+        autoCodeSplitting: false,
+        routesDirectory: 'src/paths',
+        generatedRouteTree: 'src/tree/routeTree.gen.ts',
+        enableRouteGeneration: true,
+      } as Partial<Config>,
+      withJson: false,
+    },
+    {
+      name: `inline config and "./" form relative paths`,
+      inlineConfig: {
+        target: 'solid',
+        autoCodeSplitting: true,
+        routesDirectory: './src/paths',
+        generatedRouteTree: './src/tree/routeTree.gen.ts',
+        enableRouteGeneration: true,
+      } as Partial<Config>,
+      withJson: false,
+    },
+    {
+      name: 'inline config and absolute paths',
+      inlineConfig: {
+        target: 'solid',
+        autoCodeSplitting: false,
+        routesDirectory: '/src/paths',
+        generatedRouteTree: '/src/tree/routeTree.gen.ts',
+        enableRouteGeneration: true,
+      } as Partial<Config>,
+      withJson: false,
+    },
+    {
+      name: 'json config',
+      inlineConfig: {} as Partial<Config>,
+      withJson: true,
+    },
+    {
+      name: 'combination of json and inline config',
+      inlineConfig: {
+        target: 'react',
+        autoCodeSplitting: true,
+        routesDirectory: './src/paths',
+        generatedRouteTree: './src/tree/routeTree.gen.ts',
+        enableRouteGeneration: true,
+      } as Partial<Config>,
+      withJson: true,
+    },
+  ]
+
+  it.each(testCases)('must resolve $name', ({ inlineConfig, withJson }) => {
+    const rootPath = withJson ? 'withJson' : 'withoutJson'
+    const root = path.resolve(import.meta.dirname, 'config', rootPath)
+
+    const jsonConfig = withJson
+      ? JSON.parse(readFileSync(path.resolve(root, 'tsr.config.json'), 'utf-8'))
+      : undefined
+
+    const routesPath =
+      inlineConfig.routesDirectory ??
+      jsonConfig?.routesDirectory ??
+      'src/routes'
+
+    const routeTreePath =
+      inlineConfig.generatedRouteTree ??
+      jsonConfig?.generatedRouteTree ??
+      'src/routeTree.gen.ts'
+
+    const routesDirectory = path.resolve(
+      import.meta.dirname,
+      'config',
+      rootPath,
+      routesPath,
+    )
+
+    const generatedRouteTree = path.resolve(
+      import.meta.dirname,
+      'config',
+      rootPath,
+      routeTreePath,
+    )
+
+    const resolvedConfig = getConfig(inlineConfig, root)
+
+    expect(resolvedConfig).toEqual(
+      expect.objectContaining({
+        ...jsonConfig,
+        ...inlineConfig,
+        routesDirectory,
+        generatedRouteTree,
+      }),
+    )
+  })
+})
diff --git a/packages/router-plugin/tests/config/withJson/tsr.config.json b/packages/router-plugin/tests/config/withJson/tsr.config.json
new file mode 100644
index 0000000000..367f00064c
--- /dev/null
+++ b/packages/router-plugin/tests/config/withJson/tsr.config.json
@@ -0,0 +1,6 @@
+{
+  "routesDirectory": "./src/routes",
+  "generatedRouteTree": "./src/routeTree.gen.ts",
+  "target": "solid",
+  "autoCodeSplitting": false
+}