diff --git a/src/Microsoft.Sbom.Api/Entities/ErrorType.cs b/src/Microsoft.Sbom.Api/Entities/ErrorType.cs
index 39114a33..7d05e88b 100644
--- a/src/Microsoft.Sbom.Api/Entities/ErrorType.cs
+++ b/src/Microsoft.Sbom.Api/Entities/ErrorType.cs
@@ -47,5 +47,8 @@ public enum ErrorType
     NoPackagesFound = 11,
 
     [EnumMember(Value = "Manifest file signing error")]
-    ManifestFileSigningError = 12
+    ManifestFileSigningError = 12,
+
+    [EnumMember(Value = "Invalid input file")]
+    InvalidInputFile = 13
 }
diff --git a/src/Microsoft.Sbom.Api/Executors/EnumeratorChannel.cs b/src/Microsoft.Sbom.Api/Executors/EnumeratorChannel.cs
index a09e580f..dd4db11c 100644
--- a/src/Microsoft.Sbom.Api/Executors/EnumeratorChannel.cs
+++ b/src/Microsoft.Sbom.Api/Executors/EnumeratorChannel.cs
@@ -6,6 +6,8 @@
 using System.Threading.Channels;
 using System.Threading.Tasks;
 using Microsoft.Sbom.Api.Entities;
+using Microsoft.Sbom.Api.Output.Telemetry;
+using Microsoft.Sbom.JsonAsynchronousNodeKit.Exceptions;
 using Serilog;
 
 namespace Microsoft.Sbom.Api.Executors;
@@ -42,6 +44,15 @@ async Task Enumerate()
                     await output.Writer.WriteAsync(value);
                 }
             }
+            catch (ParserException e)
+            {
+                // Don't log this here, as it will be logged by upstream error handling.
+                await errors.Writer.WriteAsync(new FileValidationResult
+                {
+                    ErrorType = ErrorType.InvalidInputFile,
+                    Path = e.Message
+                });
+            }
             catch (Exception e)
             {
                 log.Warning($"Encountered an unknown error while enumerating: {e.Message}");
diff --git a/src/Microsoft.Sbom.Api/Workflows/SBOMParserBasedValidationWorkflow.cs b/src/Microsoft.Sbom.Api/Workflows/SBOMParserBasedValidationWorkflow.cs
index 9692a3af..f0b47beb 100644
--- a/src/Microsoft.Sbom.Api/Workflows/SBOMParserBasedValidationWorkflow.cs
+++ b/src/Microsoft.Sbom.Api/Workflows/SBOMParserBasedValidationWorkflow.cs
@@ -4,6 +4,7 @@
 using System;
 using System.Collections.Generic;
 using System.Diagnostics;
+using System.IO;
 using System.Linq;
 using System.Text.Json;
 using System.Text.Json.Serialization;
@@ -109,6 +110,12 @@ public async Task<bool> RunAsync()
                         {
                             case FilesResult filesResult:
                                 (successfullyValidatedFiles, fileValidationFailures) = await filesValidator.Validate(filesResult.Files);
+                                var invalidInputFiles = fileValidationFailures.Where(f => f.ErrorType == ErrorType.InvalidInputFile).ToList();
+                                if (invalidInputFiles.Count != 0)
+                                {
+                                    throw new InvalidDataException($"Your manifest file is malformed. {invalidInputFiles.First().Path}");
+                                }
+
                                 break;
                             case PackagesResult packagesResult:
                                 var packages = packagesResult.Packages.ToList();