diff --git a/generator/nanopb_generator.py b/generator/nanopb_generator.py
index 91c8975..7519905 100755
--- a/generator/nanopb_generator.py
+++ b/generator/nanopb_generator.py
@@ -2025,6 +2025,7 @@
             sys.stderr.write("Writing to %s\n" % paths)
 
         for path, data in to_write:
+            os.makedirs(os.path.dirname(path), exist_ok=True)
             with open(path, 'w') as f:
                 f.write(data)
 
diff --git a/tests/generator_relative_paths/SConscript b/tests/generator_relative_paths/SConscript
new file mode 100644
index 0000000..d17bec7
--- /dev/null
+++ b/tests/generator_relative_paths/SConscript
@@ -0,0 +1,44 @@
+# Test correct relative paths and creation of intermediate directories
+# when input files are part of a multi-level directory structure:
+#
+# user@host:.../build$ nanopb_generator -D . -I ../proto ../proto/simple.proto
+# user@host:.../build$ nanopb_generator -D . -I ../proto ../proto/protobuf/any.proto
+#
+# should result in:
+#
+# ├── build
+# │   ├── protobuf
+# │   │   ├── any.pb.c
+# │   │   └── any.pb.h
+# │   ├── simple.pb.c
+# │   └── simple.pb.h
+# └── proto
+#     ├── protobuf
+#     │   └── any.proto
+#     └── simple.proto
+
+
+Import('env')
+import os, sys
+
+# As of 0.4.2, SCons rules still go through protoc that handles paths correctly
+# by itself. To test direct nanopb_generator usage we invoke it manually here.
+
+generator_cmd = os.path.join(env['NANOPB'], 'generator-bin', 'nanopb_generator' + env['PROGSUFFIX'])
+if os.path.exists(generator_cmd):
+    generator_cmd = env['ESCAPE'](generator_cmd)
+else:
+    generator_cmd = env['ESCAPE'](sys.executable) + " " + env['ESCAPE'](os.path.join(env['NANOPB'], 'generator', 'nanopb_generator.py'))
+
+env.Command(["build/protobuf/any.pb.h", "build/simple.pb.h", "build/protobuf/any.pb.c", "build/simple.pb.c",],
+            ["proto/protobuf/any.proto", "proto/simple.proto"],
+[
+    Delete("build/generator_relative_paths/build"),
+    Mkdir("build/generator_relative_paths/build"),
+    generator_cmd + " -Dbuild/generator_relative_paths/build -Ibuild/generator_relative_paths/proto $SOURCES"
+])
+
+env.Match("simple_pb_h_ok", ["build/simple.pb.h", "simple.expected"])
+env.Match("simple_pb_c_ok", ["build/simple.pb.c", "simple.expected"])
+env.Match("any_pb_h_ok", ["build/protobuf/any.pb.h", "any.expected"])
+env.Match("any_pb_c_ok", ["build/protobuf/any.pb.c", "any.expected"])
\ No newline at end of file
diff --git a/tests/generator_relative_paths/any.expected b/tests/generator_relative_paths/any.expected
new file mode 100644
index 0000000..ec0b2ca
--- /dev/null
+++ b/tests/generator_relative_paths/any.expected
@@ -0,0 +1 @@
+Any
diff --git a/tests/generator_relative_paths/proto/protobuf/any.proto b/tests/generator_relative_paths/proto/protobuf/any.proto
new file mode 100644
index 0000000..4932942
--- /dev/null
+++ b/tests/generator_relative_paths/proto/protobuf/any.proto
@@ -0,0 +1,154 @@
+// Protocol Buffers - Google's data interchange format
+// Copyright 2008 Google Inc.  All rights reserved.
+// https://developers.google.com/protocol-buffers/
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+//     * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+//     * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+syntax = "proto3";
+
+package google.protobuf;
+
+option csharp_namespace = "Google.Protobuf.WellKnownTypes";
+option go_package = "github.com/golang/protobuf/ptypes/any";
+option java_package = "com.google.protobuf";
+option java_outer_classname = "AnyProto";
+option java_multiple_files = true;
+option objc_class_prefix = "GPB";
+
+// `Any` contains an arbitrary serialized protocol buffer message along with a
+// URL that describes the type of the serialized message.
+//
+// Protobuf library provides support to pack/unpack Any values in the form
+// of utility functions or additional generated methods of the Any type.
+//
+// Example 1: Pack and unpack a message in C++.
+//
+//     Foo foo = ...;
+//     Any any;
+//     any.PackFrom(foo);
+//     ...
+//     if (any.UnpackTo(&foo)) {
+//       ...
+//     }
+//
+// Example 2: Pack and unpack a message in Java.
+//
+//     Foo foo = ...;
+//     Any any = Any.pack(foo);
+//     ...
+//     if (any.is(Foo.class)) {
+//       foo = any.unpack(Foo.class);
+//     }
+//
+//  Example 3: Pack and unpack a message in Python.
+//
+//     foo = Foo(...)
+//     any = Any()
+//     any.Pack(foo)
+//     ...
+//     if any.Is(Foo.DESCRIPTOR):
+//       any.Unpack(foo)
+//       ...
+//
+//  Example 4: Pack and unpack a message in Go
+//
+//      foo := &pb.Foo{...}
+//      any, err := ptypes.MarshalAny(foo)
+//      ...
+//      foo := &pb.Foo{}
+//      if err := ptypes.UnmarshalAny(any, foo); err != nil {
+//        ...
+//      }
+//
+// The pack methods provided by protobuf library will by default use
+// 'type.googleapis.com/full.type.name' as the type URL and the unpack
+// methods only use the fully qualified type name after the last '/'
+// in the type URL, for example "foo.bar.com/x/y.z" will yield type
+// name "y.z".
+//
+//
+// JSON
+// ====
+// The JSON representation of an `Any` value uses the regular
+// representation of the deserialized, embedded message, with an
+// additional field `@type` which contains the type URL. Example:
+//
+//     package google.profile;
+//     message Person {
+//       string first_name = 1;
+//       string last_name = 2;
+//     }
+//
+//     {
+//       "@type": "type.googleapis.com/google.profile.Person",
+//       "firstName": <string>,
+//       "lastName": <string>
+//     }
+//
+// If the embedded message type is well-known and has a custom JSON
+// representation, that representation will be embedded adding a field
+// `value` which holds the custom JSON in addition to the `@type`
+// field. Example (for message [google.protobuf.Duration][]):
+//
+//     {
+//       "@type": "type.googleapis.com/google.protobuf.Duration",
+//       "value": "1.212s"
+//     }
+//
+message Any {
+  // A URL/resource name that uniquely identifies the type of the serialized
+  // protocol buffer message. The last segment of the URL's path must represent
+  // the fully qualified name of the type (as in
+  // `path/google.protobuf.Duration`). The name should be in a canonical form
+  // (e.g., leading "." is not accepted).
+  //
+  // In practice, teams usually precompile into the binary all types that they
+  // expect it to use in the context of Any. However, for URLs which use the
+  // scheme `http`, `https`, or no scheme, one can optionally set up a type
+  // server that maps type URLs to message definitions as follows:
+  //
+  // * If no scheme is provided, `https` is assumed.
+  // * An HTTP GET on the URL must yield a [google.protobuf.Type][]
+  //   value in binary format, or produce an error.
+  // * Applications are allowed to cache lookup results based on the
+  //   URL, or have them precompiled into a binary to avoid any
+  //   lookup. Therefore, binary compatibility needs to be preserved
+  //   on changes to types. (Use versioned type names to manage
+  //   breaking changes.)
+  //
+  // Note: this functionality is not currently available in the official
+  // protobuf release, and it is not used for type URLs beginning with
+  // type.googleapis.com.
+  //
+  // Schemes other than `http`, `https` (or the empty scheme) might be
+  // used with implementation specific semantics.
+  //
+  string type_url = 1;
+
+  // Must be a valid serialized protocol buffer of the above specified type.
+  bytes value = 2;
+}
diff --git a/tests/generator_relative_paths/proto/simple.proto b/tests/generator_relative_paths/proto/simple.proto
new file mode 100644
index 0000000..3c6a983
--- /dev/null
+++ b/tests/generator_relative_paths/proto/simple.proto
@@ -0,0 +1,8 @@
+syntax = "proto3";
+
+import "protobuf/any.proto";
+
+message SimpleMessage {
+    google.protobuf.Any any = 1;
+}
+
diff --git a/tests/generator_relative_paths/simple.expected b/tests/generator_relative_paths/simple.expected
new file mode 100644
index 0000000..87b1d8e
--- /dev/null
+++ b/tests/generator_relative_paths/simple.expected
@@ -0,0 +1 @@
+SimpleMessage