diff --git a/.changeset/quick-eagles-impress.md b/.changeset/quick-eagles-impress.md
new file mode 100644
index 000000000..8729df039
--- /dev/null
+++ b/.changeset/quick-eagles-impress.md
@@ -0,0 +1,5 @@
+---
+'astro': patch
+---
+
+Fix inline root resolve logic
diff --git a/packages/astro/src/core/config/config.ts b/packages/astro/src/core/config/config.ts
index 0872145db..29b0bb23a 100644
--- a/packages/astro/src/core/config/config.ts
+++ b/packages/astro/src/core/config/config.ts
@@ -211,6 +211,10 @@ async function loadConfig(
 	}
 }
 
+/**
+ * `AstroInlineConfig` is a union of `AstroUserConfig` and `AstroInlineOnlyConfig`.
+ * This functions splits it up.
+ */
 function splitInlineConfig(inlineConfig: AstroInlineConfig): {
 	inlineUserConfig: AstroUserConfig;
 	inlineOnlyConfig: AstroInlineOnlyConfig;
@@ -231,6 +235,12 @@ interface ResolveConfigResult {
 	astroConfig: AstroConfig;
 }
 
+/**
+ * Resolves the Astro config with a given inline config.
+ *
+ * @param inlineConfig An inline config that takes highest priority when merging and resolving the final config.
+ * @param command The running command that uses this config. Usually 'dev' or 'build'.
+ */
 export async function resolveConfig(
 	inlineConfig: AstroInlineConfig,
 	command: string,
@@ -239,6 +249,11 @@ export async function resolveConfig(
 	const root = resolveRoot(inlineConfig.root);
 	const { inlineUserConfig, inlineOnlyConfig } = splitInlineConfig(inlineConfig);
 
+	// If the root is specified, assign the resolved path so it takes the highest priority
+	if (inlineConfig.root) {
+		inlineUserConfig.root = root;
+	}
+
 	const userConfig = await loadConfig(root, inlineOnlyConfig.configFile, fsMod);
 	const mergedConfig = mergeConfig(userConfig, inlineUserConfig);
 	const astroConfig = await validateConfig(mergedConfig, root, command);
diff --git a/packages/astro/test/units/config/config-resolve.test.js b/packages/astro/test/units/config/config-resolve.test.js
new file mode 100644
index 000000000..c3c19da64
--- /dev/null
+++ b/packages/astro/test/units/config/config-resolve.test.js
@@ -0,0 +1,18 @@
+import { expect } from 'chai';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { resolveConfig } from '../../../dist/core/config/index.js';
+
+describe('resolveConfig', () => {
+	it('resolves relative inline root correctly', async () => {
+		const { astroConfig } = await resolveConfig(
+			{
+				configFile: false,
+				root: 'relative/path',
+			},
+			'dev'
+		);
+		const expectedRoot = path.join(process.cwd(), 'relative/path/');
+		expect(fileURLToPath(astroConfig.root)).to.equal(expectedRoot);
+	});
+});