diff --git a/debian/changelog b/debian/changelog
index 124128920b..7631406a68 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+matrix-synapse-py3 (0.99.2) UNRELEASED; urgency=medium
+
+  * Fix overwriting of config settings on upgrade.
+
+ -- Synapse Packaging team <packages@matrix.org>  Wed, 20 Feb 2019 17:11:25 +0000
+
 matrix-synapse-py3 (0.99.1.1) stable; urgency=medium
 
   * New synapse release 0.99.1.1
diff --git a/debian/install b/debian/install
index 3d916a9718..43dc8c6904 100644
--- a/debian/install
+++ b/debian/install
@@ -1 +1,2 @@
 debian/log.yaml etc/matrix-synapse
+debian/manage_debconf.pl /opt/venvs/matrix-synapse/lib/
diff --git a/debian/manage_debconf.pl b/debian/manage_debconf.pl
new file mode 100755
index 0000000000..be8ed32050
--- /dev/null
+++ b/debian/manage_debconf.pl
@@ -0,0 +1,130 @@
+#!/usr/bin/perl
+#
+# Interface between our config files and the debconf database.
+#
+# Usage:
+#
+#   manage_debconf.pl <action>
+#
+# where <action> can be:
+#
+#   read:    read the configuration from the yaml into debconf
+#   update:  update the yaml config according to the debconf database
+use strict;
+use warnings;
+
+use Debconf::Client::ConfModule (qw/get set/);
+
+# map from the name of a setting in our .yaml file to the relevant debconf
+# setting.
+my %MAPPINGS=(
+    server_name => 'matrix-synapse/server-name',
+    report_stats => 'matrix-synapse/report-stats',
+);
+
+# enable debug if dpkg --debug
+my $DEBUG = $ENV{DPKG_MAINTSCRIPT_DEBUG};
+
+sub read_config {
+    my @files = @_;
+
+    foreach my $file (@files)  {
+        print STDERR "reading $file\n" if $DEBUG;
+
+        open my $FH, "<", $file or next;
+
+        # rudimentary parsing which (a) avoids having to depend on a yaml library,
+        # and (b) is tolerant of yaml errors
+        while($_ = <$FH>) {
+            while (my ($setting, $debconf) = each %MAPPINGS) {
+                $setting = quotemeta $setting;
+                if(/^${setting}\s*:(.*)$/) {
+                    my $val = $1;
+
+                    # remove leading/trailing whitespace
+                    $val =~ s/^\s*//;
+                    $val =~ s/\s*$//;
+
+                    # remove surrounding quotes
+                    if ($val =~ /^"(.*)"$/ || $val =~ /^'(.*)'$/) {
+                        $val = $1;
+                    }
+
+                    print STDERR ">> $debconf = $val\n" if $DEBUG;
+                    set($debconf, $val);
+                }
+            }
+        }
+        close $FH;
+    }
+}
+
+sub update_config {
+    my @files = @_;
+
+    my %substs = ();
+    while (my ($setting, $debconf) = each %MAPPINGS) {
+        my @res = get($debconf);
+        $substs{$setting} = $res[1] if $res[0] == 0;
+    }
+
+    foreach my $file (@files) {
+        print STDERR "checking $file\n" if $DEBUG;
+
+        open my $FH, "<", $file or next;
+
+        my $updated = 0;
+
+        # read the whole file into memory
+        my @lines = <$FH>;
+
+        while (my ($setting, $val) = each %substs) {
+            $setting = quotemeta $setting;
+
+            map {
+                if (/^${setting}\s*:\s*(.*)\s*$/) {
+                    my $current = $1;
+                    if ($val ne $current) {
+                        $_ = "${setting}: $val\n";
+                        $updated = 1;
+                    }
+                }
+            } @lines;
+        }
+        close $FH;
+
+        next unless $updated;
+
+        print STDERR "updating $file\n" if $DEBUG;
+        open $FH, ">", $file or die "unable to update $file";
+        print $FH @lines;
+        close $FH;
+    }
+}
+
+
+my $cmd = $ARGV[0];
+
+my $read = 0;
+my $update = 0;
+
+if (not $cmd) {
+    die "must specify a command to perform\n";
+} elsif ($cmd eq 'read') {
+    $read = 1;
+} elsif ($cmd eq 'update') {
+    $update = 1;
+} else {
+    die "unknown command '$cmd'\n";
+}
+
+my @files = (
+    "/etc/matrix-synapse/homeserver.yaml",
+    glob("/etc/matrix-synapse/conf.d/*.yaml"),
+);
+
+if ($read) {
+    read_config(@files);
+} elsif ($update) {
+    update_config(@files);
+}
diff --git a/debian/config b/debian/matrix-synapse-py3.config
similarity index 53%
rename from debian/config
rename to debian/matrix-synapse-py3.config
index 9fb6913298..3bda3292f1 100755
--- a/debian/config
+++ b/debian/matrix-synapse-py3.config
@@ -4,6 +4,9 @@ set -e
 
 . /usr/share/debconf/confmodule
 
+# try to update the debconf db according to whatever is in the config files
+/opt/venvs/matrix-synapse/lib/manage_debconf.pl read || true
+
 db_input high matrix-synapse/server-name || true
 db_input high matrix-synapse/report-stats || true
 db_go
diff --git a/debian/matrix-synapse-py3.postinst b/debian/matrix-synapse-py3.postinst
index 0509acd0a4..c0dd7e5534 100644
--- a/debian/matrix-synapse-py3.postinst
+++ b/debian/matrix-synapse-py3.postinst
@@ -8,19 +8,36 @@ USER="matrix-synapse"
 
 case "$1" in
   configure|reconfigure)
-    # Set server name in config file
+
+    # generate template config files if they don't exist
     mkdir -p "/etc/matrix-synapse/conf.d/"
-    db_get matrix-synapse/server-name
+    if [ ! -e "$CONFIGFILE_SERVERNAME" ]; then
+        cat > "$CONFIGFILE_SERVERNAME" <<EOF
+# This file is autogenerated, and will be recreated on upgrade if it is deleted.
+# Any changes you make will be preserved.
 
-    if [ "$RET" ]; then
-        echo "server_name: $RET" > $CONFIGFILE_SERVERNAME
+# The domain name of the server, with optional explicit port.
+# This is used by remote servers to connect to this server,
+# e.g. matrix.org, localhost:8080, etc.
+# This is also the last part of your UserID.
+#
+server_name: ''
+EOF
     fi
 
-    db_get matrix-synapse/report-stats
-    if [ "$RET" ]; then
-        echo "report_stats: $RET" > $CONFIGFILE_REPORTSTATS
+    if [ ! -e "$CONFIGFILE_REPORTSTATS" ]; then
+        cat > "$CONFIGFILE_REPORTSTATS" <<EOF
+# This file is autogenerated, and will be recreated on upgrade if it is deleted.
+# Any changes you make will be preserved.
+
+# Whether to report anonymized homeserver usage statistics.
+report_stats: false
+EOF
     fi
 
+    # update the config files according to whatever is in the debconf database
+    /opt/venvs/matrix-synapse/lib/manage_debconf.pl update
+
     if ! getent passwd $USER >/dev/null; then
       adduser --quiet --system --no-create-home --home /var/lib/matrix-synapse $USER
     fi