diff --git a/.changeset/dry-eagles-share.md b/.changeset/dry-eagles-share.md
new file mode 100644
index 00000000..caeb7fc9
--- /dev/null
+++ b/.changeset/dry-eagles-share.md
@@ -0,0 +1,5 @@
+---
+"vscode-apollo": patch
+---
+
+Fix a bug handling windows path separators in `FileSet` instances.
diff --git a/.github/workflows/E2E.yml b/.github/workflows/E2E.yml
index 890ef982..4a6e3fc5 100644
--- a/.github/workflows/E2E.yml
+++ b/.github/workflows/E2E.yml
@@ -7,26 +7,63 @@ on:
 jobs:
   test:
     name: Run E2E tests
-    runs-on: ubuntu-latest
+    runs-on: "${{ matrix.os }}"
     strategy:
       matrix:
         version: ["1.90.0", "stable", "insiders"]
+        os: [ubuntu-latest]
+        include:
+          - version: "stable"
+            os: "windows-latest"
     steps:
       - run: sudo apt update && sudo apt install -y libasound2 libgbm1 libgtk-3-0 libnss3 xvfb expect
+        if: runner.os == 'Linux'
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4
         with:
           cache: "npm"
       - run: npm install
-      - run: npm run build:production
       - run: echo 'APOLLO_KEY="service:bob-123:489fhseo4"' > ./sampleWorkspace/spotifyGraph/.env
-      - run: |
+        shell: bash
+      - name: Install & Configure Rover (Linux)
+        run: |
           expect <<EOF
           spawn ./node_modules/.bin/rover config auth --profile VSCode-E2E
           expect "Copy the key and paste it into the prompt below."
           send -- "test\n"
           expect eof
           EOF
-      - run: xvfb-run -a npm run test:extension
+        if: runner.os == 'Linux'
+      - name: Install Rover (Windows)
+        run: ./node_modules/.bin/rover.cmd --version
+        if: runner.os == 'Windows'
+      - name: Configure Rover (Windows)
+        run: |
+          [void] [System.Reflection.Assembly]::LoadWithPartialName("System.Windows.Forms")
+          Start-Process -FilePath ./node_modules/.bin/rover.cmd -ArgumentList "config","auth","--profile","VSCode-E2E"
+
+          Start-Sleep -m 1000
+
+          [System.Windows.Forms.SendKeys]::SendWait("test")
+          [System.Windows.Forms.SendKeys]::SendWait("{ENTER}")
+        if: runner.os == 'Windows'
+        shell: powershell
+      - name: Adjust configuration (Windows)
+        run: |
+          sed -i -e 's/\(bin:.*\)/\1.exe/' sampleWorkspace/rover/apollo.config.yaml
+          cat sampleWorkspace/rover/apollo.config.yaml
+          # for some reason, windows seems to ignore the jest.e2e.config.js file
+          echo "module.exports = require('./jest.e2e.config')" > jest.config.ts
+        shell: bash
+        if: runner.os == 'Windows'
+      - run: npm run build:production
+      - name: "Run Extension E2E tests (Linux)"
+        run: xvfb-run -a npm run test:extension
+        env:
+          VSCODE_VERSION: "${{ matrix.version }}"
+        if: runner.os == 'Linux'
+      - name: "Run Extension E2E tests (Windows)"
+        run: npm run test:extension
         env:
           VSCODE_VERSION: "${{ matrix.version }}"
+        if: runner.os == 'Windows'
diff --git a/src/language-server/__e2e__/rover.e2e.ts b/src/language-server/__e2e__/rover.e2e.ts
index 2d7d62ad..cbeae25d 100644
--- a/src/language-server/__e2e__/rover.e2e.ts
+++ b/src/language-server/__e2e__/rover.e2e.ts
@@ -41,6 +41,11 @@ if (test === origTest.skip) {
   );
 }
 
+if (process.platform === "win32") {
+  console.info("Skipping rover E2E tests in Windows");
+  test = origTest.skip;
+}
+
 let editor: TextEditor;
 let getPosition: GetPositionFn;
 beforeAll(async () => {
diff --git a/src/language-server/__e2e__/studioGraph.e2e.ts b/src/language-server/__e2e__/studioGraph.e2e.ts
index 9c8fb553..3cbed06d 100644
--- a/src/language-server/__e2e__/studioGraph.e2e.ts
+++ b/src/language-server/__e2e__/studioGraph.e2e.ts
@@ -63,13 +63,13 @@ test("wrong token", async () => {
 
     // currently, this logs twice, along with a full stracktrace, but no indication of where it came from
     // this should be improved on.
-    expect(output).toContain(
+    expect(output.replace(/\s/g, "")).toContain(
       `
 [GraphQL error]: HTTP fetch failed from 'kotlin': 406: Not Acceptable
 [GraphQL error]: Invalid credentials provided
 ApolloError: HTTP fetch failed from 'kotlin': 406: Not Acceptable
 Invalid credentials provided
-    at new ApolloError`.trim(),
+    at new ApolloError`.replace(/\s/g, ""),
     );
   } finally {
     await mocks.loadDefaultMocks(baseUri);
diff --git a/src/language-server/fileSet.ts b/src/language-server/fileSet.ts
index ca7862b6..91b9e50c 100644
--- a/src/language-server/fileSet.ts
+++ b/src/language-server/fileSet.ts
@@ -2,7 +2,7 @@ import { minimatch } from "minimatch";
 import { globSync } from "glob";
 import { invariant } from "../tools";
 import { URI } from "vscode-uri";
-import { normalizeURI } from "./utilities";
+import { normalizeURI, withUnixSeparator } from "./utilities";
 import { resolve } from "path";
 
 export class FileSet {
@@ -35,13 +35,13 @@ export class FileSet {
       this.includes.some((include) => {
         return minimatch(
           normalizedFilePath,
-          resolve(this.rootURI.fsPath, include),
+          withUnixSeparator(resolve(this.rootURI.fsPath, include)),
         );
       }) &&
       !this.excludes.some((exclude) => {
         return minimatch(
           normalizedFilePath,
-          resolve(this.rootURI.fsPath, exclude),
+          withUnixSeparator(resolve(this.rootURI.fsPath, exclude)),
         );
       })
     );
diff --git a/src/language-server/utilities/uri.ts b/src/language-server/utilities/uri.ts
index 2a830b30..4a746f9c 100644
--- a/src/language-server/utilities/uri.ts
+++ b/src/language-server/utilities/uri.ts
@@ -1,6 +1,6 @@
 import { URI } from "vscode-uri";
 
-const withUnixSeparator = (uriString: string) =>
+export const withUnixSeparator = (uriString: string) =>
   uriString.split(/[\/\\]/).join("/");
 
 export const normalizeURI = (uriString: string) => {