diff --git a/alot/db/manager.py b/alot/db/manager.py
index 8af6a9472..6d950ef74 100644
--- a/alot/db/manager.py
+++ b/alot/db/manager.py
@@ -72,7 +72,7 @@ def flush(self):
             raise DatabaseROError()
         if self.writequeue:
             # read notmuch's config regarding imap flag synchronization
-            sync = settings.get_notmuch_setting('maildir', 'synchronize_flags')
+            sync = settings.get_notmuch_setting('maildir', 'synchronize_flags') == 'true'
 
             # go through writequeue entries
             while self.writequeue:
diff --git a/alot/defaults/notmuch.rc b/alot/defaults/notmuch.rc
deleted file mode 100644
index f03fcda1e..000000000
--- a/alot/defaults/notmuch.rc
+++ /dev/null
@@ -1,3 +0,0 @@
-[maildir]
-synchronize_flags = False
-
diff --git a/alot/defaults/notmuch.rc.spec b/alot/defaults/notmuch.rc.spec
deleted file mode 100644
index fb94ffd04..000000000
--- a/alot/defaults/notmuch.rc.spec
+++ /dev/null
@@ -1,3 +0,0 @@
-[maildir]
-synchronize_flags = boolean(default=False)
-
diff --git a/alot/settings/manager.py b/alot/settings/manager.py
index 1361384ba..4f1e39227 100644
--- a/alot/settings/manager.py
+++ b/alot/settings/manager.py
@@ -17,7 +17,7 @@
 from ..utils import configobj as checks
 
 from .errors import ConfigError, NoMatchingAccount
-from .utils import read_config
+from .utils import read_config, read_notmuch_config
 from .utils import resolve_att
 from .theme import Theme
 
@@ -36,12 +36,13 @@ def __init__(self):
         self._accounts = None
         self._accountmap = None
         self._notmuchconfig = None
+        self._notmuchconfig_path = None
         self._config = ConfigObj()
         self._bindings = None
 
     def reload(self):
         """Reload notmuch and alot config files"""
-        self.read_notmuch_config(self._notmuchconfig.filename)
+        self.read_notmuch_config(self._notmuchconfig_path)
         self.read_config(self._config.filename)
 
     def read_notmuch_config(self, path):
@@ -50,8 +51,8 @@ def read_notmuch_config(self, path):
         :param path: path to notmuch's config file
         :type path: str
         """
-        spec = os.path.join(DEFAULTSPATH, 'notmuch.rc.spec')
-        self._notmuchconfig = read_config(path, spec)
+        self._notmuchconfig = read_notmuch_config(path)
+        self._notmuchconfig_path = path  # Set the path *after* succesful read.
 
     def _update_bindings(self, newbindings):
         assert isinstance(newbindings, Section)
@@ -275,7 +276,8 @@ def get_notmuch_setting(self, section, key, fallback=None):
         :type key: str
         :param fallback: fallback returned if key is not present
         :type fallback: str
-        :returns: config value with type as specified in the spec-file
+        :returns: the config value
+        :rtype: str
         """
         value = None
         if section in self._notmuchconfig:
diff --git a/alot/settings/utils.py b/alot/settings/utils.py
index 65942aff6..7b106b122 100644
--- a/alot/settings/utils.py
+++ b/alot/settings/utils.py
@@ -9,6 +9,7 @@
 from urwid import AttrSpec
 
 from .errors import ConfigError
+from ..helper import call_cmd
 
 
 def read_config(configpath=None, specpath=None, checks=None,
@@ -82,6 +83,40 @@ def read_config(configpath=None, specpath=None, checks=None,
     return config
 
 
+def read_notmuch_config(path):
+    """
+    Read notmuch configuration.
+
+    This function calls the command "notmuch --config {path} config list" and
+    parses its output into a ``config`` dictionary, which is then returned.
+
+    The configuration value for a key under a section can be accessed with
+    ``config[section][key]``.
+
+    The returned value is a dict ``config`` with
+
+    :param path: path to the configuration file, which is passed as
+        argument to the --config option of notmuch.
+    :type path: str
+    :raises: :class:`~alot.settings.errors.ConfigError`
+    :rtype: `dict`
+    """
+    cmd = ['notmuch', '--config', path, 'config', 'list']
+    out, err, code = call_cmd(cmd)
+    if code != 0:
+        msg = f'failed to read notmuch config with command {cmd} (exit error: {code}):\n{err}'
+        logging.error(msg)
+        raise ConfigError(msg)
+
+    config = {}
+    for line in out.splitlines():
+        left_hand, right_hand = line.split("=", maxsplit=1)
+        section, key = left_hand.split(".", maxsplit=1)
+        config.setdefault(section, {})[key] = right_hand
+
+    return config
+
+
 def resolve_att(a, fallback):
     """ replace '' and 'default' by fallback values """
     if a is None:
diff --git a/setup.py b/setup.py
index d98e6c9d0..21416affd 100755
--- a/setup.py
+++ b/setup.py
@@ -31,7 +31,6 @@
     package_data={
         'alot': [
             'defaults/alot.rc.spec',
-            'defaults/notmuch.rc.spec',
             'defaults/abook_contacts.spec',
             'defaults/default.theme',
             'defaults/default.bindings',