diff --git a/src/errors/ConfigSchemaError.js b/src/errors/ConfigSchemaError.js
new file mode 100644
index 0000000000000000000000000000000000000000..f7ef6604a353a349cd8f64d8a2f498176451c7cf
--- /dev/null
+++ b/src/errors/ConfigSchemaError.js
@@ -0,0 +1,10 @@
+class ConfigSchemaError extends Error {
+  constructor(message) {
+    super(message)
+
+    this.name = 'ConfigSchemaError'
+    this.message = `${message}`
+  }
+}
+
+module.exports = ConfigSchemaError
diff --git a/src/startServer.js b/src/startServer.js
index 06964e8de28036082e47d006d401bc3029c3825d..d556ad42d1be2c116962da0dada4bbb49a40b346 100644
--- a/src/startServer.js
+++ b/src/startServer.js
@@ -13,6 +13,7 @@ const { migrate } = require('./dbManager/migrate')
 const seedGlobalTeams = require('./startup/seedGlobalTeams')
 const ensureTempFolderExists = require('./startup/ensureTempFolderExists')
 const { runCustomStartupScripts } = require('./startup/customScripts')
+const checkConfig = require('./startup/checkConfig')
 
 let server
 
@@ -23,6 +24,7 @@ const startServer = async (app = express()) => {
 
   logInit('Coko server init tasks')
 
+  checkConfig()
   await ensureTempFolderExists()
   await migrate()
   await seedGlobalTeams()
diff --git a/src/startup/checkConfig.js b/src/startup/checkConfig.js
new file mode 100644
index 0000000000000000000000000000000000000000..cae2a0644949f161598aac171bae83f7754cd945
--- /dev/null
+++ b/src/startup/checkConfig.js
@@ -0,0 +1,19 @@
+const config = require('config')
+
+const { logTask } = require('../logger/internals')
+const ConfigSchemaError = require('../errors/ConfigSchemaError')
+
+const throwPubsweetKeyError = key => {
+  throw new ConfigSchemaError(
+    `The "${key}" key has been removed. Move all configuration that existed under "${key}" to the top level of your config.`,
+  )
+}
+
+const check = () => {
+  logTask('Checking configuration')
+
+  if (config.has('pubsweet')) throwPubsweetKeyError('pubsweet')
+  if (config.has('pubsweet-server')) throwPubsweetKeyError('pubsweet=server')
+}
+
+module.exports = check