diff --git a/src/lib/utils/options/options.ts b/src/lib/utils/options/options.ts
index ef7fbd3e7..3f3cd1f12 100644
--- a/src/lib/utils/options/options.ts
+++ b/src/lib/utils/options/options.ts
@@ -1,3 +1,4 @@
+import { isDeepStrictEqual } from 'util';
 import * as _ from 'lodash';
 import * as ts from 'typescript';
 
@@ -214,14 +215,14 @@ export class Options {
     }
 
     /**
-     * Checks if the given option has a set value or if the value is the default value.
+     * Checks if the given option's value is deeply strict equal to the default.
      * @param name
      */
     isDefault(name: keyof TypeDocAndTSOptions): boolean;
     isDefault(name: string): boolean;
     isDefault(name: string): boolean {
         // getValue will throw if the declaration does not exist.
-        return this.getValue(name) === this.getDeclaration(name)!.defaultValue;
+        return isDeepStrictEqual(this.getValue(name), this.getDefaultOptionValue(this.getDeclaration(name)!));
     }
 
     /**
@@ -317,17 +318,21 @@ export class Options {
 
     /**
      * Sets the value of a given option to its default value.
-     * @param declaration The option whoes value should be reset.
+     * @param declaration The option whose value should be reset.
      */
     private setOptionValueToDefault(declaration: Readonly<DeclarationOption>): void {
         if (declaration.scope !== ParameterScope.TypeScript) {
-            // No nead to convert the defaultValue for a map type as it has to be of a specific type
-            if (declaration.type === ParameterType.Map) {
-                this._values[declaration.name] = declaration.defaultValue;
-            } else {
-                this._values[declaration.name] = convert(declaration.defaultValue, declaration)
-                    .expect(`Failed to validate default value for ${declaration.name}`);
-            }
+            this._values[declaration.name] = this.getDefaultOptionValue(declaration);
+        }
+    }
+
+    private getDefaultOptionValue(declaration: Readonly<DeclarationOption>): unknown {
+        // No need to convert the defaultValue for a map type as it has to be of a specific type
+        if (declaration.type === ParameterType.Map) {
+            return declaration.defaultValue;
+        } else {
+            return convert(declaration.defaultValue, declaration)
+                .expect(`Failed to validate default value for ${declaration.name}`);
         }
     }
 }
diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index 07c28d01b..3cb7b7a98 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -51,14 +51,19 @@ export class TSConfigReader implements OptionsReader {
         fileToRead = resolve(fileToRead);
 
         const { config } = ts.readConfigFile(fileToRead, ts.sys.readFile);
-        const { fileNames, options, raw: { typedocOptions = {} }} = ts.parseJsonConfigFileContent(
+        const { fileNames, errors, options, raw: { typedocOptions = {} }} = ts.parseJsonConfigFileContent(
             config,
             ts.sys,
             dirname(fileToRead),
             {},
             fileToRead);
 
-        container.setValue('inputFiles', fileNames).unwrap();
+        logger?.diagnostics(errors);
+
+        if (container.isDefault('inputFiles')) {
+            container.setValue('inputFiles', fileNames).unwrap();
+        }
+
         for (const key of IGNORED) {
             delete options[key];
         }
diff --git a/src/test/utils/options/readers/data/file.ts b/src/test/utils/options/readers/data/file.ts
new file mode 100644
index 000000000..a5e460907
--- /dev/null
+++ b/src/test/utils/options/readers/data/file.ts
@@ -0,0 +1,2 @@
+// This is referenced in valid.tsconfig.json
+export const test = true;
diff --git a/src/test/utils/options/readers/data/valid.tsconfig.json b/src/test/utils/options/readers/data/valid.tsconfig.json
index fc47f601e..854836627 100644
--- a/src/test/utils/options/readers/data/valid.tsconfig.json
+++ b/src/test/utils/options/readers/data/valid.tsconfig.json
@@ -1,7 +1,12 @@
 {
+    "$schema": "http://json.schemastore.org/tsconfig",
     "compilerOptions": {
         "target": "ESNext"
     },
+    "files": [
+        // This has to specify a file that exists or TS will drop it.
+        "./file.ts"
+    ],
     "typedocOptions": {
         "help": true
     }
diff --git a/src/test/utils/options/readers/tsconfig.test.ts b/src/test/utils/options/readers/tsconfig.test.ts
index 8ed918ece..bd7f4a822 100644
--- a/src/test/utils/options/readers/tsconfig.test.ts
+++ b/src/test/utils/options/readers/tsconfig.test.ts
@@ -1,4 +1,4 @@
-import { join } from 'path';
+import { join, resolve } from 'path';
 import { deepStrictEqual as equal } from 'assert';
 
 import { TSConfigReader } from '../../../../lib/utils/options/readers';
@@ -48,4 +48,19 @@ describe('Options - TSConfigReader', () => {
         equal(options.getValue('help'), true);
         equal(options.getCompilerOptions().target, ScriptTarget.ESNext);
     });
+
+    it('Sets inputFiles if they have not been set', () => {
+        options.reset();
+        options.setValue('tsconfig', join(__dirname, 'data/valid.tsconfig.json')).unwrap();
+        options.read(new Logger());
+        equal(options.getValue('inputFiles').map(f => resolve(f)), [resolve(__dirname, './data/file.ts')]);
+    });
+
+    it('Does not set inputFiles if they have been set', () => {
+        options.reset();
+        options.setValue('tsconfig', join(__dirname, 'data/valid.tsconfig.json')).unwrap();
+        options.setValue('inputFiles', ['foo.ts']).unwrap();
+        options.read(new Logger());
+        equal(options.getValue('inputFiles'), ['foo.ts']);
+    });
 });