diff --git a/src/config.test.ts b/src/config.test.ts
index 095bef7..e1b05e9 100644
--- a/src/config.test.ts
+++ b/src/config.test.ts
@@ -157,7 +157,7 @@ describe("mergeConfigsAndTemplates", () => {
       base_url: "http://sonarr:8989",
     };
 
-    const result = await mergeConfigsAndTemplates(inputConfig, "SONARR");
+    const result = await mergeConfigsAndTemplates({}, inputConfig, "SONARR");
 
     expect(result.config.custom_formats.length).toBe(3);
     expect(result.config.quality_profiles.length).toBe(3);
@@ -197,7 +197,7 @@ describe("mergeConfigsAndTemplates", () => {
       base_url: "http://sonarr:8989",
     };
 
-    const result = await mergeConfigsAndTemplates(inputConfig, "SONARR");
+    const result = await mergeConfigsAndTemplates({}, inputConfig, "SONARR");
 
     expect(result.config.custom_formats.length).toBe(0);
     expect(result.config.quality_profiles.length).toBe(0);
@@ -236,7 +236,7 @@ describe("mergeConfigsAndTemplates", () => {
       base_url: "http://sonarr:8989",
     };
 
-    const result = await mergeConfigsAndTemplates(inputConfig, "SONARR");
+    const result = await mergeConfigsAndTemplates({}, inputConfig, "SONARR");
 
     expect(result.config.custom_formats.length).toBe(2);
     expect(result.config.quality_profiles.length).toBe(1);
@@ -282,13 +282,13 @@ describe("mergeConfigsAndTemplates", () => {
       base_url: "http://sonarr:8989",
     };
 
-    const result = await mergeConfigsAndTemplates(inputConfig, "SONARR");
+    const result = await mergeConfigsAndTemplates({}, inputConfig, "SONARR");
 
     expect(result.config.custom_formats.length).toBe(0);
     expect(result.config.quality_profiles.length).toBe(0);
   });
 
   test("should throw error for invalid input configuration", async () => {
-    await expect(mergeConfigsAndTemplates(null as any, "SONARR")).rejects.toThrow();
+    await expect(mergeConfigsAndTemplates({}, null as any, "SONARR")).rejects.toThrow();
   });
 });
diff --git a/src/config.ts b/src/config.ts
index 6dbf2ee..d3e8bd8 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -171,11 +171,12 @@ export const validateConfig = (input: InputConfigInstance): MergedConfigInstance
 /**
  * Load data from trash, recyclarr, custom configs and merge.
  * Afterwards do sanitize and check against required configuration.
- * @param value
+ * @param instanceConfig
  * @param arrType
  */
 export const mergeConfigsAndTemplates = async (
-  value: InputConfigArrInstance,
+  globalConfig: InputConfigSchema,
+  instanceConfig: InputConfigArrInstance,
   arrType: ArrType,
 ): Promise<{ config: MergedConfigInstance }> => {
   const localTemplateMap = loadLocalRecyclarrTemplate(arrType);
@@ -198,8 +199,8 @@ export const mergeConfigsAndTemplates = async (
   };
 
   // HINT: we assume customFormatDefinitions only exist in RECYCLARR
-  if (value.include) {
-    const mappedIncludes = value.include.reduce<{ recyclarr: InputConfigIncludeItem[]; trash: InputConfigIncludeItem[] }>(
+  if (instanceConfig.include) {
+    const mappedIncludes = instanceConfig.include.reduce<{ recyclarr: InputConfigIncludeItem[]; trash: InputConfigIncludeItem[] }>(
       (previous, current) => {
         switch (current.source) {
           case "TRASH":
@@ -218,7 +219,7 @@ export const mergeConfigsAndTemplates = async (
     );
 
     logger.info(
-      `Found ${value.include.length} templates to include. Mapped to [recyclarr]=${mappedIncludes.recyclarr.length}, [trash]=${mappedIncludes.trash.length} ...`,
+      `Found ${instanceConfig.include.length} templates to include. Mapped to [recyclarr]=${mappedIncludes.recyclarr.length}, [trash]=${mappedIncludes.trash.length} ...`,
     );
 
     mappedIncludes.recyclarr.forEach((e) => {
@@ -287,41 +288,55 @@ export const mergeConfigsAndTemplates = async (
   }
 
   // Config values overwrite template values
-  if (value.custom_formats) {
-    mergedTemplates.custom_formats.push(...value.custom_formats);
+  if (instanceConfig.custom_formats) {
+    mergedTemplates.custom_formats.push(...instanceConfig.custom_formats);
   }
 
-  if (value.quality_profiles) {
-    mergedTemplates.quality_profiles.push(...value.quality_profiles);
+  if (instanceConfig.quality_profiles) {
+    mergedTemplates.quality_profiles.push(...instanceConfig.quality_profiles);
   }
 
-  if (value.media_management) {
-    mergedTemplates.media_management = { ...mergedTemplates.media_management, ...value.media_management };
+  if (instanceConfig.media_management) {
+    mergedTemplates.media_management = { ...mergedTemplates.media_management, ...instanceConfig.media_management };
   }
 
-  if (value.media_naming) {
+  if (instanceConfig.media_naming) {
     mergedTemplates.media_naming_api = {
       ...mergedTemplates.media_naming_api,
-      ...(await mapConfigMediaNamingToApi(arrType, value.media_naming)),
+      ...(await mapConfigMediaNamingToApi(arrType, instanceConfig.media_naming)),
     };
   }
 
-  if (value.media_naming_api) {
-    mergedTemplates.media_naming_api = { ...mergedTemplates.media_naming_api, ...value.media_naming_api };
+  if (instanceConfig.media_naming_api) {
+    mergedTemplates.media_naming_api = { ...mergedTemplates.media_naming_api, ...instanceConfig.media_naming_api };
   }
 
-  if (value.quality_definition) {
-    mergedTemplates.quality_definition = { ...mergedTemplates.quality_definition, ...value.quality_definition };
+  if (instanceConfig.quality_definition) {
+    mergedTemplates.quality_definition = { ...mergedTemplates.quality_definition, ...instanceConfig.quality_definition };
   }
 
-  if (value.customFormatDefinitions) {
-    if (Array.isArray(value.customFormatDefinitions)) {
-      mergedTemplates.customFormatDefinitions = [...(mergedTemplates.customFormatDefinitions || []), ...value.customFormatDefinitions];
+  if (globalConfig.customFormatDefinitions) {
+    if (Array.isArray(globalConfig.customFormatDefinitions)) {
+      mergedTemplates.customFormatDefinitions = [
+        ...(mergedTemplates.customFormatDefinitions || []),
+        ...globalConfig.customFormatDefinitions,
+      ];
     } else {
       logger.warn(`CustomFormatDefinitions in config file must be an array. Ignoring.`);
     }
   }
 
+  if (instanceConfig.customFormatDefinitions) {
+    if (Array.isArray(instanceConfig.customFormatDefinitions)) {
+      mergedTemplates.customFormatDefinitions = [
+        ...(mergedTemplates.customFormatDefinitions || []),
+        ...instanceConfig.customFormatDefinitions,
+      ];
+    } else {
+      logger.warn(`CustomFormatDefinitions in instance config file must be an array. Ignoring.`);
+    }
+  }
+
   const recyclarrProfilesMerged = mergedTemplates.quality_profiles.reduce<Map<string, ConfigQualityProfile>>((p, c) => {
     const profile = p.get(c.name);
 
diff --git a/src/index.ts b/src/index.ts
index 6065910..bba9b87 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -15,13 +15,13 @@ import { calculateQualityProfilesDiff, loadQualityProfilesFromServer } from "./q
 import { cloneRecyclarrTemplateRepo } from "./recyclarr-importer";
 import { cloneTrashRepo, loadQualityDefinitionFromTrash } from "./trash-guide";
 import { ArrType } from "./types/common.types";
-import { InputConfigArrInstance } from "./types/config.types";
+import { InputConfigArrInstance, InputConfigSchema } from "./types/config.types";
 import { TrashQualityDefintion } from "./types/trashguide.types";
 
-const pipeline = async (value: InputConfigArrInstance, arrType: ArrType) => {
+const pipeline = async (globalConfig: InputConfigSchema, instanceConfig: InputConfigArrInstance, arrType: ArrType) => {
   const api = getUnifiedClient();
 
-  const { config } = await mergeConfigsAndTemplates(value, arrType);
+  const { config } = await mergeConfigsAndTemplates(globalConfig, instanceConfig, arrType);
 
   const idsToManage = calculateCFsToManage(config);
   logger.debug(Array.from(idsToManage), `CustomFormats to manage`);
@@ -157,14 +157,14 @@ const run = async () => {
     logger.info("DryRun: Running in dry-run mode!");
   }
 
-  const applicationConfig = getConfig();
+  const globalConfig = getConfig();
 
   await cloneRecyclarrTemplateRepo();
   await cloneTrashRepo();
 
   // TODO currently this has to be run sequentially because of the centrally configured api
 
-  const sonarrConfig = applicationConfig.sonarr;
+  const sonarrConfig = globalConfig.sonarr;
 
   if (sonarrConfig == null || Array.isArray(sonarrConfig) || typeof sonarrConfig !== "object" || Object.keys(sonarrConfig).length <= 0) {
     logHeading(`No Sonarr instances defined.`);
@@ -174,12 +174,12 @@ const run = async () => {
     for (const [instanceName, instance] of Object.entries(sonarrConfig)) {
       logger.info(`Processing Sonarr Instance: ${instanceName}`);
       await configureApi("SONARR", instance.base_url, instance.api_key);
-      await pipeline(instance, "SONARR");
+      await pipeline(globalConfig, instance, "SONARR");
       unsetApi();
     }
   }
 
-  const radarrConfig = applicationConfig.radarr;
+  const radarrConfig = globalConfig.radarr;
 
   if (radarrConfig == null || Array.isArray(radarrConfig) || typeof radarrConfig !== "object" || Object.keys(radarrConfig).length <= 0) {
     logHeading(`No Radarr instances defined.`);
@@ -189,12 +189,12 @@ const run = async () => {
     for (const [instanceName, instance] of Object.entries(radarrConfig)) {
       logger.info(`Processing Radarr Instance: ${instanceName}`);
       await configureApi("RADARR", instance.base_url, instance.api_key);
-      await pipeline(instance, "RADARR");
+      await pipeline(globalConfig, instance, "RADARR");
       unsetApi();
     }
   }
 
-  const whisparrConfig = applicationConfig.whisparr;
+  const whisparrConfig = globalConfig.whisparr;
 
   if (
     whisparrConfig == null ||
@@ -209,12 +209,12 @@ const run = async () => {
     for (const [instanceName, instance] of Object.entries(whisparrConfig)) {
       logger.info(`Processing Whisparr Instance: ${instanceName}`);
       await configureApi("WHISPARR", instance.base_url, instance.api_key);
-      await pipeline(instance, "WHISPARR");
+      await pipeline(globalConfig, instance, "WHISPARR");
       unsetApi();
     }
   }
 
-  const readarrConfig = applicationConfig.readarr;
+  const readarrConfig = globalConfig.readarr;
 
   if (
     readarrConfig == null ||
@@ -229,7 +229,7 @@ const run = async () => {
     for (const [instanceName, instance] of Object.entries(readarrConfig)) {
       logger.info(`Processing Readarr Instance: ${instanceName}`);
       await configureApi("READARR", instance.base_url, instance.api_key);
-      await pipeline(instance, "READARR");
+      await pipeline(globalConfig, instance, "READARR");
       unsetApi();
     }
   }