diff --git a/.ci/scripts/test_export_data_command.sh b/.ci/scripts/test_export_data_command.sh
index ab96387a0aef..224cae921658 100755
--- a/.ci/scripts/test_export_data_command.sh
+++ b/.ci/scripts/test_export_data_command.sh
@@ -21,7 +21,7 @@ python -m synapse.app.homeserver --generate-keys -c .ci/sqlite-config.yaml
 echo "--- Prepare test database"
 
 # Make sure the SQLite3 database is using the latest schema and has no pending background update.
-scripts/update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
+update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
 
 # Run the export-data command on the sqlite test database
 python -m synapse.app.admin_cmd -c .ci/sqlite-config.yaml  export-data @anon-20191002_181700-832:localhost:8800 \
@@ -41,7 +41,7 @@ fi
 
 # Port the SQLite databse to postgres so we can check command works against postgres
 echo "+++ Port SQLite3 databse to postgres"
-scripts/synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
+synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
 
 # Run the export-data command on postgres database
 python -m synapse.app.admin_cmd -c .ci/postgres-config.yaml  export-data @anon-20191002_181700-832:localhost:8800 \
diff --git a/.ci/scripts/test_synapse_port_db.sh b/.ci/scripts/test_synapse_port_db.sh
index 797904e64ca5..ec5bbd3b1ccf 100755
--- a/.ci/scripts/test_synapse_port_db.sh
+++ b/.ci/scripts/test_synapse_port_db.sh
@@ -25,17 +25,17 @@ python -m synapse.app.homeserver --generate-keys -c .ci/sqlite-config.yaml
 echo "--- Prepare test database"
 
 # Make sure the SQLite3 database is using the latest schema and has no pending background update.
-scripts/update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
+update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
 
 # Create the PostgreSQL database.
 .ci/scripts/postgres_exec.py "CREATE DATABASE synapse"
 
 echo "+++ Run synapse_port_db against test database"
-coverage run scripts/synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
+coverage run synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
 
 # We should be able to run twice against the same database.
 echo "+++ Run synapse_port_db a second time"
-coverage run scripts/synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
+coverage run synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
 
 #####
 
@@ -46,7 +46,7 @@ echo "--- Prepare empty SQLite database"
 # we do this by deleting the sqlite db, and then doing the same again.
 rm .ci/test_db.db
 
-scripts/update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
+update_synapse_database --database-config .ci/sqlite-config.yaml --run-background-updates
 
 # re-create the PostgreSQL database.
 .ci/scripts/postgres_exec.py \
@@ -54,4 +54,4 @@ scripts/update_synapse_database --database-config .ci/sqlite-config.yaml --run-b
   "CREATE DATABASE synapse"
 
 echo "+++ Run synapse_port_db against empty database"
-coverage run scripts/synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
+coverage run synapse_port_db --sqlite-database .ci/test_db.db --postgres-config .ci/postgres-config.yaml
diff --git a/docs/development/database_schema.md b/docs/development/database_schema.md
index a767d3af9fd3..d996a7caa2c6 100644
--- a/docs/development/database_schema.md
+++ b/docs/development/database_schema.md
@@ -158,9 +158,9 @@ same as integers.
 There are three separate aspects to this:
 
  * Any new boolean column must be added to the `BOOLEAN_COLUMNS` list in
-   `scripts/synapse_port_db`. This tells the port script to cast the integer
-   value from SQLite to a boolean before writing the value to the postgres
-   database.
+   `synapse/_scripts/synapse_port_db.py`. This tells the port script to cast
+   the integer value from SQLite to a boolean before writing the value to the
+   postgres database.
 
  * Before SQLite 3.23, `TRUE` and `FALSE` were not recognised as constants by
    SQLite, and the `IS [NOT] TRUE`/`IS [NOT] FALSE` operators were not
diff --git a/scripts-dev/generate_sample_config b/scripts-dev/generate_sample_config
index 4cd1d1d5b829..185e277933e3 100755
--- a/scripts-dev/generate_sample_config
+++ b/scripts-dev/generate_sample_config
@@ -10,19 +10,19 @@ SAMPLE_CONFIG="docs/sample_config.yaml"
 SAMPLE_LOG_CONFIG="docs/sample_log_config.yaml"
 
 check() {
-    diff -u "$SAMPLE_LOG_CONFIG" <(./scripts/generate_log_config) >/dev/null || return 1
+    diff -u "$SAMPLE_LOG_CONFIG" <(synapse/_scripts/generate_log_config.py) >/dev/null || return 1
 }
 
 if [ "$1" == "--check" ]; then
-    diff -u "$SAMPLE_CONFIG" <(./scripts/generate_config --header-file docs/.sample_config_header.yaml) >/dev/null || {
+    diff -u "$SAMPLE_CONFIG" <(synapse/_scripts/generate_config.py --header-file docs/.sample_config_header.yaml) >/dev/null || {
         echo -e "\e[1m\e[31m$SAMPLE_CONFIG is not up-to-date. Regenerate it with \`scripts-dev/generate_sample_config\`.\e[0m" >&2
         exit 1
     }
-    diff -u "$SAMPLE_LOG_CONFIG" <(./scripts/generate_log_config) >/dev/null || {
+    diff -u "$SAMPLE_LOG_CONFIG" <(synapse/_scripts/generate_log_config.py) >/dev/null || {
         echo -e "\e[1m\e[31m$SAMPLE_LOG_CONFIG is not up-to-date. Regenerate it with \`scripts-dev/generate_sample_config\`.\e[0m" >&2
         exit 1
     }
 else
-    ./scripts/generate_config --header-file docs/.sample_config_header.yaml -o "$SAMPLE_CONFIG"
-    ./scripts/generate_log_config -o "$SAMPLE_LOG_CONFIG"
+    synapse/_scripts/generate_config.py --header-file docs/.sample_config_header.yaml -o "$SAMPLE_CONFIG"
+    synapse/_scripts/generate_log_config.py -o "$SAMPLE_LOG_CONFIG"
 fi
diff --git a/scripts-dev/make_full_schema.sh b/scripts-dev/make_full_schema.sh
index c3c90f4ec637..f0e22d4ca25b 100755
--- a/scripts-dev/make_full_schema.sh
+++ b/scripts-dev/make_full_schema.sh
@@ -147,7 +147,7 @@ python -m synapse.app.homeserver --generate-keys -c "$SQLITE_CONFIG"
 
 # Make sure the SQLite3 database is using the latest schema and has no pending background update.
 echo "Running db background jobs..."
-scripts/update_synapse_database --database-config --run-background-updates "$SQLITE_CONFIG"
+synapse/_scripts/update_synapse_database.py --database-config --run-background-updates "$SQLITE_CONFIG"
 
 # Create the PostgreSQL database.
 echo "Creating postgres database..."
@@ -156,10 +156,10 @@ createdb --lc-collate=C --lc-ctype=C --template=template0 "$POSTGRES_DB_NAME"
 echo "Copying data from SQLite3 to Postgres with synapse_port_db..."
 if [ -z "$COVERAGE" ]; then
   # No coverage needed
-  scripts/synapse_port_db --sqlite-database "$SQLITE_DB" --postgres-config "$POSTGRES_CONFIG"
+  synapse/_scripts/synapse_port_db.py --sqlite-database "$SQLITE_DB" --postgres-config "$POSTGRES_CONFIG"
 else
   # Coverage desired
-  coverage run scripts/synapse_port_db --sqlite-database "$SQLITE_DB" --postgres-config "$POSTGRES_CONFIG"
+  coverage run synapse/_scripts/synapse_port_db.py --sqlite-database "$SQLITE_DB" --postgres-config "$POSTGRES_CONFIG"
 fi
 
 # Delete schema_version, applied_schema_deltas and applied_module_schemas tables
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
index 9a01152c156b..dd4c8478d59d 100644
--- a/snap/snapcraft.yaml
+++ b/snap/snapcraft.yaml
@@ -20,7 +20,7 @@ apps:
   generate-config:
     command: generate_config
   generate-signing-key:
-    command: generate_signing_key.py
+    command: generate_signing_key
   register-new-matrix-user:
     command: register_new_matrix_user
     plugs: [network]