diff --git a/docs/html/md__compiler.html b/docs/html/md__compiler.html
index ff3f7fe22..1b3cd1db4 100644
--- a/docs/html/md__compiler.html
+++ b/docs/html/md__compiler.html
@@ -63,8 +63,8 @@ $(document).ready(function(){initNavTree('md__compiler.html','');});
 <div class="contents">
 <div class="textblock"><p>Usage: </p><pre class="fragment">flatc [ GENERATOR OPTIONS ] [ -o PATH ] [ -I PATH ] [ -S ] FILES...
       [ -- FILES...]
-</pre><p>The files are read and parsed in order, and can contain either schemas or data (see below). Later files can make use of definitions in earlier files.</p>
-<p><code>--</code> indicates that the following files are binary files in FlatBuffer format conforming to the schema(s) indicated before it. Incompatible binary files currently will give unpredictable results (!)</p>
+</pre><p>The files are read and parsed in order, and can contain either schemas or data (see below). Data files are processed according to the definitions of the most recent schema specified.</p>
+<p><code>--</code> indicates that the following files are binary files in FlatBuffer format conforming to the schema indicated before it.</p>
 <p>Depending on the flags passed, additional files may be generated for each file processed:</p>
 <p>For any schema input files, one or more generators can be specified:</p>
 <ul>
diff --git a/docs/source/Compiler.md b/docs/source/Compiler.md
index 27ddf52e4..9d89cb104 100755
--- a/docs/source/Compiler.md
+++ b/docs/source/Compiler.md
@@ -6,12 +6,11 @@ Usage:
           [ -- FILES...]
 
 The files are read and parsed in order, and can contain either schemas
-or data (see below). Later files can make use of definitions in earlier
-files.
+or data (see below). Data files are processed according to the definitions of
+the most recent schema specified.
 
 `--` indicates that the following files are binary files in
-FlatBuffer format conforming to the schema(s) indicated before it.
-Incompatible binary files currently will give unpredictable results (!)
+FlatBuffer format conforming to the schema indicated before it.
 
 Depending on the flags passed, additional files may
 be generated for each file processed:
diff --git a/include/flatbuffers/util.h b/include/flatbuffers/util.h
index 8e5d09908..ba73d67bd 100644
--- a/include/flatbuffers/util.h
+++ b/include/flatbuffers/util.h
@@ -174,6 +174,12 @@ inline std::string StripExtension(const std::string &filepath) {
   return i != std::string::npos ? filepath.substr(0, i) : filepath;
 }
 
+// Returns the extension, if any.
+inline std::string GetExtension(const std::string &filepath) {
+  size_t i = filepath.find_last_of(".");
+  return i != std::string::npos ? filepath.substr(i + 1) : "";
+}
+
 // Return the last component of the path, after the last separator.
 inline std::string StripPath(const std::string &filepath) {
   size_t i = filepath.find_last_of(PathSeparatorSet);
diff --git a/src/flatc.cpp b/src/flatc.cpp
index 2479da12b..86de77416 100644
--- a/src/flatc.cpp
+++ b/src/flatc.cpp
@@ -79,7 +79,8 @@ const Generator generators[] = {
     flatbuffers::GeneralMakeRule },
 };
 
-const char *program_name = NULL;
+const char *program_name = nullptr;
+flatbuffers::Parser *parser = nullptr;
 
 static void Error(const std::string &err, bool usage, bool show_exe_name) {
   if (show_exe_name) printf("%s: ", program_name);
@@ -122,6 +123,7 @@ static void Error(const std::string &err, bool usage, bool show_exe_name) {
       "example: %s -c -b schema1.fbs schema2.fbs data.json\n",
       program_name);
   }
+  if (parser) delete parser;
   exit(1);
 }
 
@@ -205,7 +207,7 @@ int main(int argc, const char *argv[]) {
     Error("no options: specify one of -c -g -j -t -b etc.", true);
 
   // Now process the files:
-  flatbuffers::Parser parser(opts.strict_json, proto_mode);
+  parser = new flatbuffers::Parser(opts.strict_json, proto_mode);
   for (auto file_it = filenames.begin();
             file_it != filenames.end();
           ++file_it) {
@@ -216,8 +218,8 @@ int main(int argc, const char *argv[]) {
       bool is_binary = static_cast<size_t>(file_it - filenames.begin()) >=
                        binary_files_from;
       if (is_binary) {
-        parser.builder_.Clear();
-        parser.builder_.PushFlatBuffer(
+        parser->builder_.Clear();
+        parser->builder_.PushFlatBuffer(
           reinterpret_cast<const uint8_t *>(contents.c_str()),
           contents.length());
         if (!raw_binary) {
@@ -226,30 +228,37 @@ int main(int argc, const char *argv[]) {
           // does not contain a file identifier.
           // We'd expect that typically any binary used as a file would have
           // such an identifier, so by default we require them to match.
-          if (!parser.file_identifier_.length()) {
+          if (!parser->file_identifier_.length()) {
             Error("current schema has no file_identifier: cannot test if \"" +
                  *file_it +
                  "\" matches the schema, use --raw-binary to read this file"
                  " anyway.");
           } else if (!flatbuffers::BufferHasIdentifier(contents.c_str(),
-                                             parser.file_identifier_.c_str())) {
+                                             parser->file_identifier_.c_str())) {
             Error("binary \"" +
                  *file_it +
                  "\" does not have expected file_identifier \"" +
-                 parser.file_identifier_ +
+                 parser->file_identifier_ +
                  "\", use --raw-binary to read this file anyway.");
           }
         }
       } else {
+        if (flatbuffers::GetExtension(*file_it) == "fbs") {
+          // If we're processing multiple schemas, make sure to start each
+          // one from scratch. If it depends on previous schemas it must do
+          // so explicitly using an include.
+          delete parser;
+          parser = new flatbuffers::Parser(opts.strict_json, proto_mode);
+        }
         auto local_include_directory = flatbuffers::StripFileName(*file_it);
         include_directories.push_back(local_include_directory.c_str());
         include_directories.push_back(nullptr);
-        if (!parser.Parse(contents.c_str(), &include_directories[0],
+        if (!parser->Parse(contents.c_str(), &include_directories[0],
                           file_it->c_str()))
-          Error(parser.error_, false, false);
+          Error(parser->error_, false, false);
         if (schema_binary) {
-          parser.Serialize();
-          parser.file_extension_ = reflection::SchemaExtension();
+          parser->Serialize();
+          parser->file_extension_ = reflection::SchemaExtension();
         }
         include_directories.pop_back();
         include_directories.pop_back();
@@ -280,11 +289,8 @@ int main(int argc, const char *argv[]) {
       }
 
       if (proto_mode) GenerateFBS(parser, output_path, filebase, opts);
-
-      // We do not want to generate code for the definitions in this file
-      // in any files coming up next.
-      parser.MarkGenerated();
   }
 
+  delete parser;
   return 0;
 }
diff --git a/src/idl_parser.cpp b/src/idl_parser.cpp
index 233eeceef..f2b7fc9c4 100644
--- a/src/idl_parser.cpp
+++ b/src/idl_parser.cpp
@@ -1072,10 +1072,9 @@ bool Parser::SetRootType(const char *name) {
 }
 
 void Parser::MarkGenerated() {
-  // Since the Parser object retains definitions across files, we must
-  // ensure we only output code for definitions once, in the file they are first
-  // declared. This function marks all existing definitions as having already
-  // been generated.
+  // This function marks all existing definitions as having already
+  // been generated, which signals no code for included files should be
+  // generated.
   for (auto it = enums_.vec.begin();
            it != enums_.vec.end(); ++it) {
     (*it)->generated = true;