diff --git a/src/api/prune.ts b/src/api/prune.ts
index 9799f2b6ca..6639211074 100644
--- a/src/api/prune.ts
+++ b/src/api/prune.ts
@@ -53,6 +53,7 @@ export async function prune(maybeOpts?: PnpmOptions): Promise<void> {
       store: ctx.storePath,
       storeIndex: ctx.storeIndex,
       pruneStore: true,
+      bin: opts.bin,
     })
   }
 }
diff --git a/src/api/removeOrphanPkgs.ts b/src/api/removeOrphanPkgs.ts
index 90a6bc0078..45c2856f24 100644
--- a/src/api/removeOrphanPkgs.ts
+++ b/src/api/removeOrphanPkgs.ts
@@ -12,6 +12,7 @@ export default async function removeOrphanPkgs (
   opts: {
     oldShrinkwrap: Shrinkwrap,
     newShrinkwrap: Shrinkwrap,
+    bin: string,
     prefix: string,
     store: string,
     storeIndex: Store,
@@ -29,7 +30,10 @@ export default async function removeOrphanPkgs (
       name: depName[0],
       dev: Boolean(opts.oldShrinkwrap.devDependencies && opts.oldShrinkwrap.devDependencies[depName[0]]),
       optional: Boolean(opts.oldShrinkwrap.optionalDependencies && opts.oldShrinkwrap.optionalDependencies[depName[0]]),
-    }, rootModules)
+    }, {
+      modules: rootModules,
+      bin: opts.bin,
+    })
   }))
 
   const oldPkgIds = R.keys(opts.oldShrinkwrap.packages).map(depPath => dp.resolve(opts.oldShrinkwrap.registry, depPath))
diff --git a/src/api/uninstall.ts b/src/api/uninstall.ts
index 8b7484a5ce..b2a2864b38 100644
--- a/src/api/uninstall.ts
+++ b/src/api/uninstall.ts
@@ -72,6 +72,7 @@ export async function uninstallInContext (pkgsToUninstall: string[], ctx: PnpmCo
     prefix: ctx.root,
     store: ctx.storePath,
     storeIndex: ctx.storeIndex,
+    bin: opts.bin,
   })
   const privateShrinkwrap = makePartialPrivateShrinkwrap
     ? pruneShrinkwrap(ctx.privateShrinkwrap, pkg)
@@ -84,7 +85,10 @@ export async function uninstallInContext (pkgsToUninstall: string[], ctx: PnpmCo
     layoutVersion: LAYOUT_VERSION,
     independentLeaves: opts.independentLeaves,
   })
-  await removeOuterLinks(pkgsToUninstall, path.join(ctx.root, 'node_modules'), {storePath: ctx.storePath})
+  await removeOuterLinks(pkgsToUninstall, path.join(ctx.root, 'node_modules'), {
+    storePath: ctx.storePath,
+    bin: opts.bin,
+  })
 
   logger('summary').info()
 }
@@ -94,6 +98,7 @@ async function removeOuterLinks (
   modules: string,
   opts: {
     storePath: string,
+    bin: string,
   }
 ) {
   // These packages are not in package.json, they were just linked in not installed
@@ -103,7 +108,10 @@ async function removeOuterLinks (
         name: pkgToUninstall,
         dev: false,
         optional: false,
-      }, modules)
+      }, {
+        modules,
+        bin: opts.bin,
+      })
     }
   }
 }
diff --git a/src/link/index.ts b/src/link/index.ts
index d23f4a2a99..ad9ad6fc04 100644
--- a/src/link/index.ts
+++ b/src/link/index.ts
@@ -61,6 +61,7 @@ export default async function (
     prefix: opts.root,
     store: opts.storePath,
     storeIndex: opts.storeIndex,
+    bin: opts.bin,
   })
 
   let flatResolvedDeps =  R.values(pkgsToLink).filter(dep => !opts.skipped.has(dep.id))
diff --git a/src/removeTopDependency.ts b/src/removeTopDependency.ts
index e079942863..ee89c1b8c3 100644
--- a/src/removeTopDependency.ts
+++ b/src/removeTopDependency.ts
@@ -10,11 +10,14 @@ export default async function removeTopDependency (
     dev: boolean,
     optional: boolean,
   },
-  modules: string
+  opts: {
+    modules: string,
+    bin: string,
+  }
 ) {
   const results = await Promise.all([
-    removeBins(dependency.name, modules),
-    rimraf(path.join(modules, dependency.name)),
+    removeBins(dependency.name, opts),
+    rimraf(path.join(opts.modules, dependency.name)),
   ])
 
   const uninstalledPkg = results[0]
@@ -27,14 +30,20 @@ export default async function removeTopDependency (
   })
 }
 
-async function removeBins (uninstalledPkg: string, modules: string) {
-  const uninstalledPkgPath = path.join(modules, uninstalledPkg)
+async function removeBins (
+  uninstalledPkg: string,
+  opts: {
+    modules: string,
+    bin: string,
+  }
+) {
+  const uninstalledPkgPath = path.join(opts.modules, uninstalledPkg)
   const uninstalledPkgJson = await safeReadPkgFromDir(uninstalledPkgPath)
 
   if (!uninstalledPkgJson) return
   const cmds = await binify(uninstalledPkgJson, uninstalledPkgPath)
   await Promise.all(
-    cmds.map(cmd => path.join(modules, '.bin', cmd.name)).map(rimraf)
+    cmds.map(cmd => path.join(opts.bin, cmd.name)).map(rimraf)
   )
 
   return uninstalledPkgJson