diff --git a/packages/coverage-istanbul/src/provider.ts b/packages/coverage-istanbul/src/provider.ts
index 480a54d47b775..84e4f77514eb0 100644
--- a/packages/coverage-istanbul/src/provider.ts
+++ b/packages/coverage-istanbul/src/provider.ts
@@ -386,6 +386,11 @@ export class IstanbulCoverageProvider
       resolve(this.ctx.config.root, file),
     )
 
+    const viteNodeServers = [
+      this.ctx.vitenode,
+      ...this.ctx.projects.map(project => project.vitenode),
+    ]
+
     if (this.ctx.config.changed) {
       includedFiles = (this.ctx.config.related || []).filter(file =>
         includedFiles.includes(file),
@@ -396,16 +401,29 @@ export class IstanbulCoverageProvider
       .filter(file => !coveredFiles.includes(file))
       .sort()
 
-    const cacheKey = new Date().getTime()
     const coverageMap = libCoverage.createCoverageMap({})
 
+    // Make sure file is not served from cache so that instrumenter loads up requested file coverage
+    const cacheKey = new Date().getTime()
+
     // Note that these cannot be run parallel as synchronous instrumenter.lastFileCoverage
     // returns the coverage of the last transformed file
     for (const [index, filename] of uncoveredFiles.entries()) {
       debug('Uncovered file %s %d/%d', filename, index, uncoveredFiles.length)
 
-      // Make sure file is not served from cache so that instrumenter loads up requested file coverage
-      await this.ctx.vitenode.transformRequest(`${filename}?v=${cacheKey}`)
+      for (const vitenode of viteNodeServers) {
+        try {
+          await vitenode.transformRequest(`${filename}?v=${cacheKey}`)
+          continue
+        }
+        catch (error) {
+          // Try transforming with next ViteNode server, unless last
+          if (viteNodeServers.indexOf(vitenode) === viteNodeServers.length - 1) {
+            throw error
+          }
+        }
+      }
+
       const lastCoverage = this.instrumenter.lastFileCoverage()
       coverageMap.addFileCoverage(lastCoverage)
     }
diff --git a/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts b/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts
new file mode 100644
index 0000000000000..956a61258a685
--- /dev/null
+++ b/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts
@@ -0,0 +1,48 @@
+import { Plugin, defineWorkspace } from "vitest/config";
+import MagicString from "magic-string";
+import { readFileSync } from "fs";
+
+export default defineWorkspace([
+  {
+    test: {
+      name: 'normal',
+      include: ['fixtures/test/math.test.ts']
+    },
+  },
+  {
+    test: {
+      name: 'special',
+      include: ['fixtures/test/custom-syntax.test.ts']
+    },
+    plugins: [customFilePlugin()]
+  }
+])
+
+function customFilePlugin(): Plugin {
+  return {
+    name: 'load-custom-files',
+    load(id) {
+      const filename = id.split("?")[0]
+
+      if(filename.endsWith(".custom")) {
+        const content = readFileSync(filename, 'utf8')
+
+        const s = new MagicString(content)
+        s.replaceAll('<function covered>', `
+function covered() {
+  return "Custom file loaded!"
+}`.trim());
+
+        s.replaceAll('<function uncovered>', `
+function uncovered() {
+  return "This should be uncovered!"
+}`.trim());
+
+        s.replaceAll('<default export covered>', 'export default covered()');
+        s.replaceAll('<default export uncovered>', 'export default uncovered()');
+
+        return { code: s.toString(), map: s.generateMap({ hires: 'boundary'})}
+      }
+    },
+  }
+}
diff --git a/test/coverage-test/fixtures/src/covered.custom b/test/coverage-test/fixtures/src/covered.custom
new file mode 100644
index 0000000000000..095b52aa44c8f
--- /dev/null
+++ b/test/coverage-test/fixtures/src/covered.custom
@@ -0,0 +1,5 @@
+<function covered>
+
+<function uncovered>
+
+<default export covered>
diff --git a/test/coverage-test/fixtures/src/uncovered.custom b/test/coverage-test/fixtures/src/uncovered.custom
new file mode 100644
index 0000000000000..f4e16be2968b7
--- /dev/null
+++ b/test/coverage-test/fixtures/src/uncovered.custom
@@ -0,0 +1,3 @@
+<function uncovered>
+
+<default export uncovered>
diff --git a/test/coverage-test/fixtures/test/custom-syntax.test.ts b/test/coverage-test/fixtures/test/custom-syntax.test.ts
new file mode 100644
index 0000000000000..d4b08f589fd41
--- /dev/null
+++ b/test/coverage-test/fixtures/test/custom-syntax.test.ts
@@ -0,0 +1,8 @@
+import { expect, test } from 'vitest'
+
+// @ts-expect-error -- untyped
+import output from '../src/covered.custom'
+
+test('custom file loads fine', () => {
+  expect(output).toMatch('Custom file loaded!')
+})
diff --git a/test/coverage-test/test/all.test.ts b/test/coverage-test/test/all.test.ts
index 063072e1f3dbf..c6bb23bf88e21 100644
--- a/test/coverage-test/test/all.test.ts
+++ b/test/coverage-test/test/all.test.ts
@@ -4,7 +4,7 @@ import { readCoverageMap, runVitest, test } from '../utils'
 test('{ all: true } includes uncovered files', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
-    exclude: ['**/virtual-files-**'],
+    exclude: ['**/virtual-files-**', '**/custom-syntax**'],
     coverage: {
       include: ['fixtures/src/**'],
       all: true,
@@ -25,7 +25,7 @@ test('{ all: true } includes uncovered files', async () => {
 test('{ all: false } excludes uncovered files', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
-    exclude: ['**/virtual-files-**'],
+    exclude: ['**/virtual-files-**', '**/custom-syntax**'],
     coverage: {
       include: ['fixtures/src/**'],
       all: false,
diff --git a/test/coverage-test/test/changed.test.ts b/test/coverage-test/test/changed.test.ts
index 33ed43d6d139f..55db075df6d01 100644
--- a/test/coverage-test/test/changed.test.ts
+++ b/test/coverage-test/test/changed.test.ts
@@ -29,6 +29,7 @@ afterAll(() => {
 test('{ changed: "HEAD" }', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
+    exclude: ['**/custom-syntax**'],
     changed: 'HEAD',
     coverage: {
       include: ['fixtures/src/**'],
diff --git a/test/coverage-test/test/workspace.multi-transform.test.ts b/test/coverage-test/test/workspace.multi-transform.test.ts
new file mode 100644
index 0000000000000..d8aa54a8bef0b
--- /dev/null
+++ b/test/coverage-test/test/workspace.multi-transform.test.ts
@@ -0,0 +1,25 @@
+import { expect } from 'vitest'
+import { readCoverageMap, runVitest, test } from '../utils'
+
+test('{ all: true } includes uncovered files that require custom transform', async () => {
+  await runVitest({
+    workspace: 'fixtures/configs/vitest.workspace.multi-transforms.ts',
+    coverage: {
+      all: true,
+      extension: ['.ts', '.custom'],
+      reporter: 'json',
+      include: ['**/*.custom', '**/math.ts'],
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/covered.custom",
+      "<process-cwd>/fixtures/src/math.ts",
+      "<process-cwd>/fixtures/src/uncovered.custom",
+    ]
+  `)
+})