diff --git a/package.json b/package.json
index 1544f8a0..987763e0 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "unipept-desktop",
-    "version": "2.0.0-alpha.0",
+    "version": "2.0.0-alpha.1",
     "productName": "Unipept Desktop",
     "private": false,
     "author": "Unipept Team (Ghent University)",
diff --git a/src/logic/application/ApplicationMigration.ts b/src/logic/application/ApplicationMigration.ts
new file mode 100644
index 00000000..af4e4be3
--- /dev/null
+++ b/src/logic/application/ApplicationMigration.ts
@@ -0,0 +1,12 @@
+/**
+ * For each version upgrade of the application that requires changes to the existing configuration, a new migrator
+ * that adheres to this interface can be implemented. This migrator will then be executed upon first opening a new
+ * version of the application.
+ */
+export default interface ApplicationMigration {
+    /**
+     * This method is called when the application is updated from one version to the next. All changes to the
+     * configuration of the application that apply to this specific version upgrade should be applied here.
+     */
+    upgrade(): Promise<void>;
+}
diff --git a/src/logic/application/ApplicationMigrationPreviousToV200alpha1.ts b/src/logic/application/ApplicationMigrationPreviousToV200alpha1.ts
new file mode 100644
index 00000000..72b8790e
--- /dev/null
+++ b/src/logic/application/ApplicationMigrationPreviousToV200alpha1.ts
@@ -0,0 +1,16 @@
+import ApplicationMigration from "@/logic/application/ApplicationMigration";
+import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
+import { app } from "@electron/remote";
+
+/**
+ * The default path of the application that's used for storing custom databases changed in version 2.0.0-alpha.1 of
+ * the application and needs to be reset here.
+ */
+export default class ApplicationMigrationPreviousToV200alpha1 implements ApplicationMigration {
+    public async upgrade(): Promise<void> {
+        // Reset the configuration back to the default value.
+        const configManager = new ConfigurationManager(app);
+        const defaultConfig = await configManager.getDefaultConfiguration();
+        await configManager.writeConfiguration(defaultConfig);
+    }
+}
diff --git a/src/logic/application/ApplicationMigrator.ts b/src/logic/application/ApplicationMigrator.ts
new file mode 100644
index 00000000..591654e4
--- /dev/null
+++ b/src/logic/application/ApplicationMigrator.ts
@@ -0,0 +1,17 @@
+import ApplicationMigration from "@/logic/application/ApplicationMigration";
+import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
+import ApplicationMigrationPreviousToV200alpha1 from "@/logic/application/ApplicationMigrationPreviousToV200alpha1";
+
+export default class ApplicationMigrator {
+    public async runMigrations(): Promise<void> {
+        const configManager = new ConfigurationManager();
+        const config = await configManager.readConfiguration();
+
+        // This key was only introduced in v2.0.0-alpha.1 of the application. If it's not present or invalid, we need
+        // to run the corresponding migration.
+        if (!config.configurationAppVersion) {
+            const migration = new ApplicationMigrationPreviousToV200alpha1();
+            await migration.upgrade();
+        }
+    }
+}
diff --git a/src/logic/application/BootstrapApplication.ts b/src/logic/application/BootstrapApplication.ts
index a299b363..6a12de38 100644
--- a/src/logic/application/BootstrapApplication.ts
+++ b/src/logic/application/BootstrapApplication.ts
@@ -3,7 +3,7 @@ import Configuration from "@/logic/configuration/Configuration";
 import { NetworkConfiguration, QueueManager } from "unipept-web-components";
 import DockerCommunicator from "@/logic/communication/docker/DockerCommunicator";
 import { Store } from "vuex";
-import CustomDatabaseManager from "@/logic/filesystem/docker/CustomDatabaseManager";
+import ApplicationMigrator from "@/logic/application/ApplicationMigrator";
 
 /**
  * This class provides functions that need to be run when the application is started. All steps that are necessary for
@@ -20,6 +20,7 @@ export default class BootstrapApplication {
      * Start and load the different components required for the application to function properly.
      */
     public async loadApplicationComponents(): Promise<void> {
+        await this.runApplicationMigrations();
         const config = await this.initializeConfiguration();
         this.initializeApi(config);
         this.initializeWorkers(config);
@@ -61,4 +62,9 @@ export default class BootstrapApplication {
     private initializeProcessing(config: Configuration): Promise<void> {
         return this.store.dispatch("initializeAssayQueue");
     }
+
+    private runApplicationMigrations(): Promise<void> {
+        const applicationMigrator = new ApplicationMigrator();
+        return applicationMigrator.runMigrations();
+    }
 }
diff --git a/src/logic/configuration/Configuration.ts b/src/logic/configuration/Configuration.ts
index 060e50d8..45519b2c 100644
--- a/src/logic/configuration/Configuration.ts
+++ b/src/logic/configuration/Configuration.ts
@@ -3,4 +3,6 @@ export default interface Configuration {
     maxParallelRequests: number;
     dockerConfigurationSettings: string;
     customDbStorageLocation: string;
+    // The version of the application that was used to create this configuration.
+    configurationAppVersion: string;
 }
diff --git a/src/logic/configuration/ConfigurationManager.ts b/src/logic/configuration/ConfigurationManager.ts
index 36468580..2b72f7f1 100644
--- a/src/logic/configuration/ConfigurationManager.ts
+++ b/src/logic/configuration/ConfigurationManager.ts
@@ -79,7 +79,8 @@ export default class ConfigurationManager {
             maxParallelRequests: 3,
             dockerConfigurationSettings:
                 Utils.isWindows() ? DockerCommunicator.WINDOWS_DEFAULT_SETTINGS : DockerCommunicator.UNIX_DEFAULT_SETTINGS,
-            customDbStorageLocation: customDbDir
+            customDbStorageLocation: customDbDir,
+            configurationAppVersion: this.app.getVersion()
         }
     }
 
diff --git a/src/logic/filesystem/database/DatabaseMigratorV4ToV5.ts b/src/logic/filesystem/database/DatabaseMigratorV4ToV5.ts
index 6b57855e..482873e1 100644
--- a/src/logic/filesystem/database/DatabaseMigratorV4ToV5.ts
+++ b/src/logic/filesystem/database/DatabaseMigratorV4ToV5.ts
@@ -9,21 +9,12 @@ import v4_to_v5 from "raw-loader!@/db/migrations/v4_to_v5.sql";
  * that were used for the analysis of a specific sample. These details are required by the application to check if the
  * selected custom database is available for analysis (or not).
  *
- * The migrator will also reset the default configuration values of the application since important changes have been
- * made to these default values since the last version (the default Docker settings for Windows-systems have changed
- * for example).
- *
  * @author Pieter Verschaffelt
  */
 export default class DatabaseMigratorV4ToV5 implements DatabaseMigrator {
     constructor(private readonly projectLocation: string) {}
 
     public async upgrade(database: Database.Database): Promise<void> {
-        // Reset the configuration back to the default value.
-        const configManager = new ConfigurationManager();
-        const defaultConfig = await configManager.getDefaultConfiguration();
-        await configManager.writeConfiguration(defaultConfig);
-
         // Now also migrate the SQL-database itself. For this to work, we need to read in all data and metadata for the
         // assays and convert to the newest database format. These data and metadata files will be temporarily kept
         // in memory.