diff --git a/examples/configuration.nix b/examples/configuration.nix
index 85c44eb..0b61906 100644
--- a/examples/configuration.nix
+++ b/examples/configuration.nix
@@ -71,11 +71,13 @@
   ## WARNING
   # If you use lnd, you should manually backup your wallet mnemonic
   # seed. This will allow you to recover on-chain funds. You can run the
-  # following command after the lnd service starts:
-  # scp bitcoin-node:/secrets/lnd-seed-mnemonic ./secrets/lnd-seed-mnemonic
+  # following commands after the lnd service starts:
+  #   mkdir -p ./backups/lnd/
+  #   scp bitcoin-node:/var/lib/lnd/lnd-seed-mnemonic ./backups/lnd/
+  #
   # You should also backup your channel state after opening new channels.
   # This will allow you to recover off-chain funds, by force-closing channels.
-  # scp bitcoin-node:/var/lib/lnd/chain/bitcoin/mainnet/channel.backup /my-backup-path/channel.backup
+  #   scp bitcoin-node:/var/lib/lnd/chain/bitcoin/mainnet/channel.backup ./backups/lnd/
 
   ### SPARK WALLET
   # Enable this module to use spark-wallet, a minimalistic wallet GUI for
@@ -229,5 +231,6 @@
   # The nix-bitcoin release version that your config is compatible with.
   # When upgrading to a backwards-incompatible release, nix-bitcoin will display an
   # an error and provide hints for migrating your config to the new release.
-  nix-bitcoin.configVersion = "0.0.30";
+  nix-bitcoin.configVersion = "0.0.41";
+
 }
diff --git a/modules/backups.nix b/modules/backups.nix
index 2669620..6209d64 100644
--- a/modules/backups.nix
+++ b/modules/backups.nix
@@ -4,7 +4,6 @@ with lib;
 
 let
   cfg = config.services.backups;
-  secretsDir = config.nix-bitcoin.secretsDir;
 
   filelist = pkgs.writeText "filelist.txt" ''
     ${optionalString (!cfg.with-bulk-data) "- ${config.services.bitcoind.dataDir}/blocks"}
@@ -12,7 +11,6 @@ let
     ${config.services.bitcoind.dataDir}
     ${config.services.clightning.dataDir}
     ${config.services.lnd.dataDir}
-    ${secretsDir}/lnd-seed-mnemonic
     ${optionalString (!cfg.with-bulk-data) "- ${config.services.liquidd.dataDir}/*/blocks"}
     ${optionalString (!cfg.with-bulk-data) "- ${config.services.liquidd.dataDir}/*/chainstate"}
     ${config.services.liquidd.dataDir}
@@ -20,8 +18,8 @@ let
     ${config.services.nbxplorer.dataDir}
     ${config.services.btcpayserver.dataDir}
     ${config.services.joinmarket.dataDir}
-    ${secretsDir}/jm-wallet-seed
     ${config.services.postgresqlBackup.location}/btcpaydb.sql.gz
+    ${optionalString config.nix-bitcoin.generateSecrets "${config.nix-bitcoin.secretsDir}"}
     /var/lib/tor
     # Extra files
     ${cfg.extraFiles}
diff --git a/modules/joinmarket.nix b/modules/joinmarket.nix
index 1dcb83a..8f46652 100644
--- a/modules/joinmarket.nix
+++ b/modules/joinmarket.nix
@@ -240,20 +240,19 @@ in {
         '';
         # Generating wallets (jmclient/wallet.py) is only supported for mainnet or testnet
         ExecStartPost = mkIf (bitcoind.network == "mainnet")
-          (nbLib.privileged "joinmarket-create-wallet" ''
+          (nbLib.script "joinmarket-create-wallet" ''
             walletname=wallet.jmdat
             wallet=${cfg.dataDir}/wallets/$walletname
             if [[ ! -f $wallet ]]; then
               echo "Create wallet"
               pw=$(cat "${secretsDir}"/jm-wallet-password)
               cd ${cfg.dataDir}
-              if ! ${pkgs.utillinux}/bin/runuser -u ${cfg.user} -- \
-                     ${nbPkgs.joinmarket}/bin/jm-genwallet --datadir=${cfg.dataDir} $walletname $pw \
+              if ! ${nbPkgs.joinmarket}/bin/jm-genwallet --datadir=${cfg.dataDir} $walletname $pw \
                      | grep 'recovery_seed' \
                      | cut -d ':' -f2 \
-                     | (umask u=r,go=; cat > "${secretsDir}/jm-wallet-seed"); then
+                     | (umask u=r,go=; cat > jm-wallet-seed); then
                 echo "wallet creation failed"
-                rm -f "$wallet" "${secretsDir}/jm-wallet-seed"
+                rm -f "$wallet" jm-wallet-seed
                 exit 1
               fi
             fi
diff --git a/modules/lnd.nix b/modules/lnd.nix
index aa6aada..00493a5 100644
--- a/modules/lnd.nix
+++ b/modules/lnd.nix
@@ -200,32 +200,28 @@ in {
         ExecStartPost = let
           restUrl = "https://${cfg.restAddress}:${toString cfg.restPort}/v1";
         in [
-          # Run fully privileged for secrets dir write access
-          (nbLib.privileged "lnd-create-mnemonic" ''
+          (nbLib.script "lnd-create-wallet" ''
             attempts=250
             while ! { exec 3>/dev/tcp/${cfg.restAddress}/${toString cfg.restPort} && exec 3>&-; } &>/dev/null; do
                   ((attempts-- == 0)) && { echo "lnd REST service unreachable"; exit 1; }
                   sleep 0.1
             done
 
-            mnemonic=${secretsDir}/lnd-seed-mnemonic
-            if [[ ! -f $mnemonic ]]; then
-              echo Create lnd seed
-              umask u=r,go=
-              ${pkgs.curl}/bin/curl -s \
-                --cacert ${secretsDir}/lnd-cert \
-                -X GET ${restUrl}/genseed | ${pkgs.jq}/bin/jq -c '.cipher_seed_mnemonic' > "$mnemonic"
-            fi
-            chown ${cfg.user}: "$mnemonic"
-          '')
-          (nbLib.script "lnd-create-wallet" ''
             if [[ ! -f ${networkDir}/wallet.db ]]; then
-              echo Create lnd wallet
+              mnemonic="${cfg.dataDir}/lnd-seed-mnemonic"
+              if [[ ! -f "$mnemonic" ]]; then
+                echo Create lnd seed
+                umask u=r,go=
+                ${pkgs.curl}/bin/curl -s \
+                  --cacert ${secretsDir}/lnd-cert \
+                  -X GET ${restUrl}/genseed | ${pkgs.jq}/bin/jq -c '.cipher_seed_mnemonic' > "$mnemonic"
+              fi
 
+              echo Create lnd wallet
               ${pkgs.curl}/bin/curl -s --output /dev/null --show-error \
                 --cacert ${secretsDir}/lnd-cert \
                 -X POST -d "{\"wallet_password\": \"$(cat ${secretsDir}/lnd-wallet-password | tr -d '\n' | base64 -w0)\", \
-                \"cipher_seed_mnemonic\": $(cat ${secretsDir}/lnd-seed-mnemonic | tr -d '\n')}" \
+                \"cipher_seed_mnemonic\": $(cat "$mnemonic" | tr -d '\n')}" \
                 ${restUrl}/initwallet
 
               # Guarantees that RPC calls with cfg.cli succeed after the service is started
@@ -248,9 +244,8 @@ in {
             while ! { exec 3>/dev/tcp/${cfg.rpcAddress}/${toString cfg.rpcPort}; } &>/dev/null; do
               sleep 0.1
             done
-
           '')
-          # Run fully privileged for chown
+          # Setting macaroon permission for other users needs root permissions
           (nbLib.privileged "lnd-create-macaroons" ''
             umask ug=r,o=
             ${lib.concatMapStrings (macaroon: ''
diff --git a/modules/versioning.nix b/modules/versioning.nix
index f06a593..f34eaac 100644
--- a/modules/versioning.nix
+++ b/modules/versioning.nix
@@ -69,6 +69,28 @@ let
     (mkOnionServiceChange "clightning")
     (mkOnionServiceChange "lnd")
     (mkOnionServiceChange "btcpayserver")
+    {
+      version = "0.0.41";
+      condition = config.services.lnd.enable || config.services.joinmarket.enable;
+      message = let
+        secretsDir = config.nix-bitcoin.secretsDir;
+        lnd = config.services.lnd;
+        jm = config.services.joinmarket;
+      in ''
+        Secret files generated by services at runtime are now stored in the service
+        data dirs instead of the global secrets dir.
+
+        To migrate, run the following Bash script as root on your nix-bitcoin node:
+
+          if [[ -e ${secretsDir}/lnd-seed-mnemonic ]]; then
+            install -o ${lnd.user} -g ${lnd.group} -m400 "${secretsDir}/lnd-seed-mnemonic" "${lnd.dataDir}"
+          fi
+          if [[ -e ${secretsDir}/jm-wallet-seed ]]; then
+            install -o ${jm.user} -g ${jm.group} -m400 "${secretsDir}/jm-wallet-seed" "${jm.dataDir}"
+          fi
+          rm -f "${secretsDir}"/{lnd-seed-mnemonic,jm-wallet-seed}
+      '';
+    }
   ];
 
   incompatibleChanges = optionals
diff --git a/test/tests.py b/test/tests.py
index dd37785..48cc4ca 100644
--- a/test/tests.py
+++ b/test/tests.py
@@ -326,16 +326,22 @@ def _():
     files = {
         "bitcoind": "var/lib/bitcoind/test/wallet.dat",
         "clightning": "var/lib/clightning/bitcoin/hsm_secret",
-        "lnd": "secrets/lnd-seed-mnemonic",
-        "joinmarket": "secrets/jm-wallet-seed",
+        "lnd": "var/lib/lnd/lnd-seed-mnemonic",
+        "joinmarket": "var/lib/joinmarket/jm-wallet-seed",
         "btcpayserver": "var/backup/postgresql/btcpaydb.sql.gz",
     }
     actual_files = succeed(f"{run_duplicity} list-current-files file:///var/lib/localBackups")
 
-    for test, file in files.items():
-        if test in enabled_tests and file not in actual_files:
+    def assert_file_exists(file):
+        if file not in actual_files:
             raise Exception(f"Backup file '{file}' is missing.")
 
+    for test, file in files.items():
+        if test in enabled_tests:
+            assert_file_exists(file)
+
+    assert_file_exists("secrets/lnd-wallet-password")
+
 
 # Impure: restarts services
 @test("banlist-and-restart")