diff --git a/synapse/config/_base.py b/synapse/config/_base.py
index 21d110c82d..20778973d5 100644
--- a/synapse/config/_base.py
+++ b/synapse/config/_base.py
@@ -354,8 +354,8 @@ class Config(object):
                     config_file.write("# vim:ft=yaml\n\n")
                     config_file.write(config_str)
 
-                config = yaml.safe_load(config_str)
-                obj.invoke_all("generate_files", config)
+                config_dict = yaml.safe_load(config_str)
+                obj.generate_missing_files(config_dict, config_dir_path)
 
                 print(
                     (
@@ -390,7 +390,7 @@ class Config(object):
         )
 
         if generate_missing_configs:
-            obj.generate_missing_files(config_dict)
+            obj.generate_missing_files(config_dict, config_dir_path)
             return None
 
         obj.parse_config_dict(
@@ -466,8 +466,8 @@ class Config(object):
             data_dir_path=data_dir_path,
         )
 
-    def generate_missing_files(self, config_dict):
-        self.invoke_all("generate_files", config_dict)
+    def generate_missing_files(self, config_dict, config_dir_path):
+        self.invoke_all("generate_files", config_dict, config_dir_path)
 
 
 def find_config_files(search_paths):
diff --git a/synapse/config/key.py b/synapse/config/key.py
index e58638f708..5ec465b196 100644
--- a/synapse/config/key.py
+++ b/synapse/config/key.py
@@ -65,13 +65,18 @@ class TrustedKeyServer(object):
 
 
 class KeyConfig(Config):
-    def read_config(self, config, **kwargs):
+    def read_config(self, config, config_dir_path, **kwargs):
         # the signing key can be specified inline or in a separate file
         if "signing_key" in config:
             self.signing_key = read_signing_keys([config["signing_key"]])
         else:
-            self.signing_key_path = config["signing_key_path"]
-            self.signing_key = self.read_signing_key(self.signing_key_path)
+            signing_key_path = config.get("signing_key_path")
+            if signing_key_path is None:
+                signing_key_path = os.path.join(
+                    config_dir_path, config["server_name"] + ".signing.key"
+                )
+
+            self.signing_key = self.read_signing_key(signing_key_path)
 
         self.old_signing_keys = self.read_old_signing_keys(
             config.get("old_signing_keys", {})
@@ -237,8 +242,15 @@ class KeyConfig(Config):
                 )
         return keys
 
-    def generate_files(self, config):
-        signing_key_path = config["signing_key_path"]
+    def generate_files(self, config, config_dir_path):
+        if "signing_key" in config:
+            return
+
+        signing_key_path = config.get("signing_key_path")
+        if signing_key_path is None:
+            signing_key_path = os.path.join(
+                config_dir_path, config["server_name"] + ".signing.key"
+            )
 
         if not self.path_exists(signing_key_path):
             print("Generating signing key file %s" % (signing_key_path,))
diff --git a/synapse/config/logger.py b/synapse/config/logger.py
index 153a137517..3e05f49aba 100644
--- a/synapse/config/logger.py
+++ b/synapse/config/logger.py
@@ -133,7 +133,7 @@ class LoggingConfig(Config):
             help="Do not redirect stdout/stderr to the log",
         )
 
-    def generate_files(self, config):
+    def generate_files(self, config, config_dir_path):
         log_config = config.get("log_config")
         if log_config and not os.path.exists(log_config):
             log_file = self.abspath("homeserver.log")
diff --git a/synapse/config/repository.py b/synapse/config/repository.py
index 15a19e0911..43e6c4921f 100644
--- a/synapse/config/repository.py
+++ b/synapse/config/repository.py
@@ -91,7 +91,9 @@ class ContentRepositoryConfig(Config):
         self.max_image_pixels = self.parse_size(config.get("max_image_pixels", "32M"))
         self.max_spider_size = self.parse_size(config.get("max_spider_size", "10M"))
 
-        self.media_store_path = self.ensure_directory(config["media_store_path"])
+        self.media_store_path = self.ensure_directory(
+            config.get("media_store_path", "media_store")
+        )
 
         backup_media_store_path = config.get("backup_media_store_path")
 
@@ -148,7 +150,7 @@ class ContentRepositoryConfig(Config):
                 (provider_class, parsed_config, wrapper_config)
             )
 
-        self.uploads_path = self.ensure_directory(config["uploads_path"])
+        self.uploads_path = self.ensure_directory(config.get("uploads_path", "uploads"))
         self.dynamic_thumbnails = config.get("dynamic_thumbnails", False)
         self.thumbnail_requirements = parse_thumbnail_requirements(
             config.get("thumbnail_sizes", DEFAULT_THUMBNAIL_SIZES)