diff --git a/descriptors.go b/descriptors.go
index 1c101af..04e8d44 100644
--- a/descriptors.go
+++ b/descriptors.go
@@ -19,9 +19,10 @@ type descriptorSet struct {
 	seen        map[string]struct{}
 	ignoreFiles map[string]struct{}
 	descProto   string
+	includeDir  string
 }
 
-func newDescriptorSet(ignoreFiles []string, d string) *descriptorSet {
+func newDescriptorSet(ignoreFiles []string, d string, i string) *descriptorSet {
 	ifm := make(map[string]struct{}, len(ignoreFiles))
 	for _, ignore := range ignoreFiles {
 		ifm[ignore] = struct{}{}
@@ -30,6 +31,7 @@ func newDescriptorSet(ignoreFiles []string, d string) *descriptorSet {
 		seen:        make(map[string]struct{}),
 		ignoreFiles: ifm,
 		descProto:   d,
+		includeDir:  i,
 	}
 }
 
@@ -56,7 +58,7 @@ func (d *descriptorSet) add(descs ...*descriptor.FileDescriptorProto) {
 //
 // This is equivalent to the following command:
 //
-// cat merged.pb | protoc --decode google.protobuf.FileDescriptorSet /path/to/google/protobuf/descriptor.proto
+// cat merged.pb | protoc -I /path/to --decode google.protobuf.FileDescriptorSet /path/to/google/protobuf/descriptor.proto
 func (d *descriptorSet) marshalTo(w io.Writer) error {
 	p, err := proto.Marshal(&d.merged)
 	if err != nil {
@@ -65,6 +67,8 @@ func (d *descriptorSet) marshalTo(w io.Writer) error {
 
 	args := []string{
 		"protoc",
+		"-I",
+		d.includeDir,
 		"--decode",
 		"google.protobuf.FileDescriptorSet",
 		d.descProto,
diff --git a/main.go b/main.go
index e75875d..a6f4ddd 100644
--- a/main.go
+++ b/main.go
@@ -70,7 +70,7 @@ func main() {
 		}
 	}
 
-	descProto, err := descriptorProto(c.Includes.After)
+	descProto, includeDir, err := descriptorProto(c.Includes.After)
 	if err != nil {
 		log.Fatalln(err)
 	}
@@ -78,7 +78,7 @@ func main() {
 	// Aggregate descriptors for each descriptor prefix.
 	descriptorSets := map[string]*descriptorSet{}
 	for _, stable := range c.Descriptors {
-		descriptorSets[stable.Prefix] = newDescriptorSet(stable.IgnoreFiles, descProto)
+		descriptorSets[stable.Prefix] = newDescriptorSet(stable.IgnoreFiles, descProto, includeDir)
 	}
 
 	shouldGenerateDescriptors := func(p string) bool {
@@ -342,17 +342,17 @@ func gopathJoin(gopath, element string) string {
 // descriptorProto returns the full path to google/protobuf/descriptor.proto
 // which might be different depending on whether it was installed. The argument
 // is the list of paths to check.
-func descriptorProto(paths []string) (string, error) {
+func descriptorProto(paths []string) (string, string, error) {
 	const descProto = "google/protobuf/descriptor.proto"
 
 	for _, dir := range paths {
 		file := path.Join(dir, descProto)
 		if _, err := os.Stat(file); err == nil {
-			return file, err
+			return file, dir, err
 		}
 	}
 
-	return "", fmt.Errorf("File %q not found (looked in: %v)", descProto, paths)
+	return "", "", fmt.Errorf("File %q not found (looked in: %v)", descProto, paths)
 }
 
 var errVendorNotFound = fmt.Errorf("no vendor dir found")