diff --git a/.changeset/fair-days-rest.md b/.changeset/fair-days-rest.md
new file mode 100644
index 0000000..19e4d2a
--- /dev/null
+++ b/.changeset/fair-days-rest.md
@@ -0,0 +1,6 @@
+---
+"@manypkg/cli": patch
+"@manypkg/get-packages": patch
+---
+
+Fixed getting correct packages in pnpm workspaces with exclude rules.
diff --git a/__fixtures__/pnpm-exclude-workspace-case/package.json b/__fixtures__/pnpm-exclude-workspace-case/package.json
new file mode 100644
index 0000000..67f0141
--- /dev/null
+++ b/__fixtures__/pnpm-exclude-workspace-case/package.json
@@ -0,0 +1,6 @@
+{
+  "private": true,
+  "name": "pnpm-exclude-workspace-case",
+  "description": "pnpm exclude rule workspace work",
+  "version": "1.0.0"
+}
diff --git a/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-a/package.json b/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-a/package.json
new file mode 100644
index 0000000..d0375cd
--- /dev/null
+++ b/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-a/package.json
@@ -0,0 +1,7 @@
+{
+  "name": "pnpm-exclude-workspace-case-pkg-a",
+  "version": "1.0.0",
+  "dependencies": {
+    "pnpm-exclude-workspace-case-pkg-b": "1.0.0"
+  }
+}
diff --git a/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-b/package.json b/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-b/package.json
new file mode 100644
index 0000000..d093e10
--- /dev/null
+++ b/__fixtures__/pnpm-exclude-workspace-case/packages/pkg-b/package.json
@@ -0,0 +1,5 @@
+  
+{
+  "name": "pnpm-exclude-workspace-case-pkg-b",
+  "version": "1.0.0"
+}
diff --git a/__fixtures__/pnpm-exclude-workspace-case/packages/pnpm-exclude-workspace-case/package.json b/__fixtures__/pnpm-exclude-workspace-case/packages/pnpm-exclude-workspace-case/package.json
new file mode 100644
index 0000000..6a92fad
--- /dev/null
+++ b/__fixtures__/pnpm-exclude-workspace-case/packages/pnpm-exclude-workspace-case/package.json
@@ -0,0 +1,5 @@
+  
+{
+  "name": "pnpm-exclude-workspace-case-excluded-pkg",
+  "version": "1.0.0"
+}
diff --git a/__fixtures__/pnpm-exclude-workspace-case/pnpm-workspace.yaml b/__fixtures__/pnpm-exclude-workspace-case/pnpm-workspace.yaml
new file mode 100644
index 0000000..4aa6ae4
--- /dev/null
+++ b/__fixtures__/pnpm-exclude-workspace-case/pnpm-workspace.yaml
@@ -0,0 +1,5 @@
+packages:
+  - 'packages/**'
+  # exclude packages that are inside myself name directories
+  - '!**/pnpm-exclude-workspace-case/**'
+  
\ No newline at end of file
diff --git a/packages/get-packages/src/index.test.ts b/packages/get-packages/src/index.test.ts
index 5fb5eb7..03db99d 100644
--- a/packages/get-packages/src/index.test.ts
+++ b/packages/get-packages/src/index.test.ts
@@ -69,6 +69,19 @@ let runTests = (getPackages: GetPackages) => {
     expect(allPackages.tool).toEqual("pnpm");
   });
 
+  it("should resolve workspace for pnpm with exclude rules", async () => {
+    const allPackages = await getPackages(f.copy("pnpm-exclude-workspace-case"));
+
+    expect(allPackages.packages[0].packageJson.name).toEqual(
+      "pnpm-exclude-workspace-case-pkg-a"
+    );
+    expect(allPackages.packages[1].packageJson.name).toEqual(
+      "pnpm-exclude-workspace-case-pkg-b"
+    );
+    expect(allPackages.packages.length).toEqual(2);
+    expect(allPackages.tool).toEqual("pnpm");
+  })
+
   it("should resolve workspaces for lerna", async () => {
     const allPackages = await getPackages(f.copy("lerna-workspace-base"));
 
diff --git a/packages/get-packages/src/index.ts b/packages/get-packages/src/index.ts
index 78c8107..a281049 100644
--- a/packages/get-packages/src/index.ts
+++ b/packages/get-packages/src/index.ts
@@ -110,13 +110,13 @@ export async function getPackages(dir: string): Promise<Packages> {
     };
   }
 
-  const directories = await globby(tool.packageGlobs, {
+  const relativeDirectories = await globby(tool.packageGlobs, {
     cwd,
     onlyDirectories: true,
-    absolute: true,
     expandDirectories: false,
     ignore: ["**/node_modules"]
   });
+  const directories = relativeDirectories.map(p => path.resolve(cwd, p))
 
   let pkgJsonsMissingNameField: Array<string> = [];
 
@@ -234,13 +234,13 @@ export function getPackagesSync(dir: string): Packages {
       packages: [root]
     };
   }
-  const directories = globbySync(tool.packageGlobs, {
+  const relativeDirectories = globbySync(tool.packageGlobs, {
     cwd,
     onlyDirectories: true,
-    absolute: true,
     expandDirectories: false,
     ignore: ["**/node_modules"]
   });
+  const directories = relativeDirectories.map(p => path.resolve(cwd, p))
 
   let pkgJsonsMissingNameField: Array<string> = [];