diff --git a/src/BenchmarkDotNet/Running/BuildPartition.cs b/src/BenchmarkDotNet/Running/BuildPartition.cs
index 4ffc48d6c8..d7fb9bc8a8 100644
--- a/src/BenchmarkDotNet/Running/BuildPartition.cs
+++ b/src/BenchmarkDotNet/Running/BuildPartition.cs
@@ -1,6 +1,7 @@
 using System;
 using System.IO;
 using System.Reflection;
+using System.Threading;
 using BenchmarkDotNet.Characteristics;
 using BenchmarkDotNet.Configs;
 using BenchmarkDotNet.Environments;
@@ -18,12 +19,20 @@ namespace BenchmarkDotNet.Running
 {
     public class BuildPartition
     {
+        // We use an auto-increment global counter instead of Guid to guarantee uniqueness per benchmark run (Guid has a small chance to collide),
+        // assuming there are fewer than 4 billion build partitions (a safe assumption).
+        internal static int s_partitionCounter;
+
         public BuildPartition(BenchmarkBuildInfo[] benchmarks, IResolver resolver)
         {
             Resolver = resolver;
             RepresentativeBenchmarkCase = benchmarks[0].BenchmarkCase;
             Benchmarks = benchmarks;
-            ProgramName = benchmarks[0].Config.Options.IsSet(ConfigOptions.KeepBenchmarkFiles) ? RepresentativeBenchmarkCase.Job.FolderInfo : Guid.NewGuid().ToString();
+            // Combine the benchmark's assembly name, folder info, and build partition id.
+            string benchmarkAssemblyName = RepresentativeBenchmarkCase.Descriptor.Type.Assembly.GetName().Name;
+            string folderInfo = RepresentativeBenchmarkCase.Job.FolderInfo;
+            int id = Interlocked.Increment(ref s_partitionCounter);
+            ProgramName = $"{benchmarkAssemblyName}-{folderInfo}-{id}";
             LogBuildOutput = benchmarks[0].Config.Options.IsSet(ConfigOptions.LogBuildOutput);
             GenerateMSBuildBinLog = benchmarks[0].Config.Options.IsSet(ConfigOptions.GenerateMSBuildBinLog);
         }
diff --git a/tests/BenchmarkDotNet.IntegrationTests/InProcessEmitTest.cs b/tests/BenchmarkDotNet.IntegrationTests/InProcessEmitTest.cs
index 6ae599e0b6..76a665d4de 100644
--- a/tests/BenchmarkDotNet.IntegrationTests/InProcessEmitTest.cs
+++ b/tests/BenchmarkDotNet.IntegrationTests/InProcessEmitTest.cs
@@ -10,6 +10,7 @@
 using BenchmarkDotNet.Jobs;
 using BenchmarkDotNet.Loggers;
 using BenchmarkDotNet.Reports;
+using BenchmarkDotNet.Running;
 using BenchmarkDotNet.Tests.Loggers;
 using BenchmarkDotNet.Tests.XUnit;
 using BenchmarkDotNet.Toolchains.InProcess.Emit;
@@ -68,10 +69,13 @@ private void DiffEmit(Summary summary)
             if (!Portability.RuntimeInformation.IsFullFramework)
                 return;
 
-            var caseName = summary.BenchmarksCases.First().Job.ToString();
+            var benchmarkCase = summary.BenchmarksCases.First();
+            var caseName = $"{benchmarkCase.Descriptor.Type.Assembly.GetName().Name}-{benchmarkCase.Job.FolderInfo}";
+            // The benchmark config built jobs with 2 toolchains, 1 InProcessEmit and 1 Roslyn,
+            // so we need to subtract 1 from the partition counter to obtain the emit output.
             NaiveRunnableEmitDiff.RunDiff(
-                $@"{caseName}.exe",
-                $@"{caseName}Emitted.dll",
+                $@"{caseName}-{BuildPartition.s_partitionCounter}.exe",
+                $@"{caseName}-{BuildPartition.s_partitionCounter - 1}Emitted.dll",
                 ConsoleLogger.Default);
         }