diff --git a/release_notes.md b/release_notes.md
index df9fc9ab68..68af6f153a 100644
--- a/release_notes.md
+++ b/release_notes.md
@@ -18,5 +18,6 @@
 - Worker termination path updated with sanitized logging (#10367)
 - Avoid redundant DiagnosticEvents error message (#10395)
 - Added logic to shim older versions of the .NET Worker JsonFunctionProvider to ensure backwards compatibility (#10410)
+- Added fallback behavior to ensure in-proc payload compatibility with "dotnet-isolated" as the `FUNCTIONS_WORKER_RUNTIME` value (#10439)
 - Migrated Scale Metrics to use `Azure.Data.Tables` SDK (#10276)
   - Added support for Identity-based connections
\ No newline at end of file
diff --git a/src/WebJobs.Script/Config/FunctionsHostingConfigOptions.cs b/src/WebJobs.Script/Config/FunctionsHostingConfigOptions.cs
index 844eb0992c..9e15db85fb 100644
--- a/src/WebJobs.Script/Config/FunctionsHostingConfigOptions.cs
+++ b/src/WebJobs.Script/Config/FunctionsHostingConfigOptions.cs
@@ -183,6 +183,14 @@ internal bool ThrowOnMissingFunctionsWorkerRuntime
             }
         }
 
+        internal bool WorkerRuntimeStrictValidationEnabled
+        {
+            get
+            {
+                return GetFeatureAsBooleanOrDefault(RpcWorkerConstants.WorkerRuntimeStrictValidationEnabled, false);
+            }
+        }
+
         /// <summary>
         /// Gets feature by name.
         /// </summary>
diff --git a/src/WebJobs.Script/Diagnostics/DiagnosticEventConstants.cs b/src/WebJobs.Script/Diagnostics/DiagnosticEventConstants.cs
index f150a705a6..2669a22a6b 100644
--- a/src/WebJobs.Script/Diagnostics/DiagnosticEventConstants.cs
+++ b/src/WebJobs.Script/Diagnostics/DiagnosticEventConstants.cs
@@ -31,5 +31,8 @@ internal static class DiagnosticEventConstants
 
         public const string NonHISSecretLoaded = "AZFD0012";
         public const string NonHISSecretLoadedHelpLink = "https://aka.ms/functions-non-his-secrets";
+
+        public const string WorkerRuntimeDoesNotMatchWithFunctionMetadataErrorCode = "AZFD0013";
+        public const string WorkerRuntimeDoesNotMatchWithFunctionMetadataHelpLink = "https://aka.ms/functions-invalid-worker-runtime";
     }
 }
diff --git a/src/WebJobs.Script/Host/ScriptHost.cs b/src/WebJobs.Script/Host/ScriptHost.cs
index dee3061b5f..9d4e5d2e68 100644
--- a/src/WebJobs.Script/Host/ScriptHost.cs
+++ b/src/WebJobs.Script/Host/ScriptHost.cs
@@ -773,14 +773,50 @@ private void TrySetDirectType(FunctionMetadata metadata)
             }
         }
 
+        // Ensure customer deployed application payload matches with the worker runtime configured for the function app and log a warning if not.
+        // If a customer has "dotnet-isolated" worker runtime configured for the function app, and then they deploy an in-proc app payload, this will warn/error
+        // If there is a mismatch, the method will return false, else true.
+        private static bool ValidateAndLogRuntimeMismatch(IEnumerable<FunctionMetadata> functionMetadata, string workerRuntime, IOptions<FunctionsHostingConfigOptions> hostingConfigOptions, ILogger logger)
+        {
+            if (functionMetadata != null && functionMetadata.Any() && !Utility.ContainsAnyFunctionMatchingWorkerRuntime(functionMetadata, workerRuntime))
+            {
+                var languages = string.Join(", ", functionMetadata.Select(f => f.Language).Distinct()).Replace(DotNetScriptTypes.DotNetAssembly, RpcWorkerConstants.DotNetLanguageWorkerName);
+                var baseMessage = $"The '{EnvironmentSettingNames.FunctionWorkerRuntime}' is set to '{workerRuntime}', which does not match the worker runtime metadata found in the deployed function app artifacts. The deployed artifacts are for '{languages}'. See {DiagnosticEventConstants.WorkerRuntimeDoesNotMatchWithFunctionMetadataHelpLink} for more information.";
+
+                if (hostingConfigOptions.Value.WorkerRuntimeStrictValidationEnabled)
+                {
+                    logger.LogDiagnosticEventError(DiagnosticEventConstants.WorkerRuntimeDoesNotMatchWithFunctionMetadataErrorCode, baseMessage, DiagnosticEventConstants.WorkerRuntimeDoesNotMatchWithFunctionMetadataHelpLink, null);
+                    throw new HostInitializationException(baseMessage);
+                }
+
+                var warningMessage = baseMessage + " The application will continue to run, but may throw an exception in the future.";
+                logger.LogDiagnosticEventWarning(DiagnosticEventConstants.WorkerRuntimeDoesNotMatchWithFunctionMetadataErrorCode, warningMessage, DiagnosticEventConstants.WorkerRuntimeDoesNotMatchWithFunctionMetadataHelpLink, null);
+                return false;
+            }
+
+            return true;
+        }
+
         internal async Task<Collection<FunctionDescriptor>> GetFunctionDescriptorsAsync(IEnumerable<FunctionMetadata> functions, IEnumerable<FunctionDescriptorProvider> descriptorProviders, string workerRuntime, CancellationToken cancellationToken)
         {
             Collection<FunctionDescriptor> functionDescriptors = new Collection<FunctionDescriptor>();
             if (!cancellationToken.IsCancellationRequested)
             {
+                bool throwOnWorkerRuntimeAndPayloadMetadataMismatch = true;
+                // this dotnet isolated specific logic is temporary to ensure in-proc payload compatibility with "dotnet-isolated" as the FUNCTIONS_WORKER_RUNTIME value.
+                if (string.Equals(workerRuntime, RpcWorkerConstants.DotNetIsolatedLanguageWorkerName, StringComparison.OrdinalIgnoreCase))
+                {
+                    bool payloadMatchesWorkerRuntime = ValidateAndLogRuntimeMismatch(functions, workerRuntime, _hostingConfigOptions, _logger);
+                    if (!payloadMatchesWorkerRuntime)
+                    {
+                        UpdateFunctionMetadataLanguageForDotnetAssembly(functions, workerRuntime);
+                        throwOnWorkerRuntimeAndPayloadMetadataMismatch = false; // we do not want to throw an exception in this case
+                    }
+                }
+
                 var httpFunctions = new Dictionary<string, HttpTriggerAttribute>();
 
-                Utility.VerifyFunctionsMatchSpecifiedLanguage(functions, workerRuntime, _environment.IsPlaceholderModeEnabled(), _isHttpWorker, cancellationToken);
+                Utility.VerifyFunctionsMatchSpecifiedLanguage(functions, workerRuntime, _environment.IsPlaceholderModeEnabled(), _isHttpWorker, cancellationToken, throwOnMismatch: throwOnWorkerRuntimeAndPayloadMetadataMismatch);
 
                 foreach (FunctionMetadata metadata in functions)
                 {
@@ -819,6 +855,17 @@ internal async Task<Collection<FunctionDescriptor>> GetFunctionDescriptorsAsync(
             return functionDescriptors;
         }
 
+        private static void UpdateFunctionMetadataLanguageForDotnetAssembly(IEnumerable<FunctionMetadata> functions, string workerRuntime)
+        {
+            foreach (var function in functions)
+            {
+                if (function.Language == DotNetScriptTypes.DotNetAssembly)
+                {
+                    function.Language = workerRuntime;
+                }
+            }
+        }
+
         internal static void ValidateFunction(FunctionDescriptor function, Dictionary<string, HttpTriggerAttribute> httpFunctions, IEnvironment environment)
         {
             var httpTrigger = function.HttpTriggerAttribute;
diff --git a/src/WebJobs.Script/Utility.cs b/src/WebJobs.Script/Utility.cs
index 8c51c4a78e..8297f85ab8 100644
--- a/src/WebJobs.Script/Utility.cs
+++ b/src/WebJobs.Script/Utility.cs
@@ -629,7 +629,7 @@ internal static bool TryReadFunctionConfig(string scriptDir, out string json, IF
             return true;
         }
 
-        internal static void VerifyFunctionsMatchSpecifiedLanguage(IEnumerable<FunctionMetadata> functions, string workerRuntime, bool isPlaceholderMode, bool isHttpWorker, CancellationToken cancellationToken)
+        internal static void VerifyFunctionsMatchSpecifiedLanguage(IEnumerable<FunctionMetadata> functions, string workerRuntime, bool isPlaceholderMode, bool isHttpWorker, CancellationToken cancellationToken, bool throwOnMismatch = true)
         {
             cancellationToken.ThrowIfCancellationRequested();
 
@@ -646,7 +646,10 @@ internal static void VerifyFunctionsMatchSpecifiedLanguage(IEnumerable<FunctionM
                 }
                 else
                 {
-                    throw new HostInitializationException($"Did not find functions with language [{workerRuntime}].");
+                    if (throwOnMismatch)
+                    {
+                        throw new HostInitializationException($"Did not find functions with language [{workerRuntime}].");
+                    }
                 }
             }
         }
@@ -748,10 +751,20 @@ private static bool ContainsFunctionWithWorkerRuntime(IEnumerable<FunctionMetada
             {
                 return functions.Any(f => dotNetLanguages.Any(l => l.Equals(f.Language, StringComparison.OrdinalIgnoreCase)));
             }
+
+            return ContainsAnyFunctionMatchingWorkerRuntime(functions, workerRuntime);
+        }
+
+        /// <summary>
+        /// Inspect the functions metadata to determine if at least one function is of the specified worker runtime.
+        /// </summary>
+        internal static bool ContainsAnyFunctionMatchingWorkerRuntime(IEnumerable<FunctionMetadata> functions, string workerRuntime)
+        {
             if (functions != null && functions.Any())
             {
                 return functions.Any(f => !string.IsNullOrEmpty(f.Language) && f.Language.Equals(workerRuntime, StringComparison.OrdinalIgnoreCase));
             }
+
             return false;
         }
 
diff --git a/src/WebJobs.Script/Workers/Rpc/FunctionRegistration/RpcFunctionInvocationDispatcher.cs b/src/WebJobs.Script/Workers/Rpc/FunctionRegistration/RpcFunctionInvocationDispatcher.cs
index a4de3c1012..af22114a1b 100644
--- a/src/WebJobs.Script/Workers/Rpc/FunctionRegistration/RpcFunctionInvocationDispatcher.cs
+++ b/src/WebJobs.Script/Workers/Rpc/FunctionRegistration/RpcFunctionInvocationDispatcher.cs
@@ -40,6 +40,9 @@ internal class RpcFunctionInvocationDispatcher : IFunctionInvocationDispatcher
         private readonly Lazy<Task<int>> _maxProcessCount;
         private readonly IOptions<FunctionsHostingConfigOptions> _hostingConfigOptions;
         private readonly IHostMetrics _hostMetrics;
+        private readonly TimeSpan _defaultProcessStartupInterval = TimeSpan.FromSeconds(5);
+        private readonly TimeSpan _defaultProcessRestartInterval = TimeSpan.FromSeconds(5);
+        private readonly TimeSpan _defaultProcessShutdownInterval = TimeSpan.FromSeconds(5);
 
         private IScriptEventManager _eventManager;
         private IWebHostRpcWorkerChannelManager _webHostLanguageWorkerChannelManager;
@@ -308,9 +311,9 @@ public async Task InitializeAsync(IEnumerable<FunctionMetadata> functions, Cance
             }
             else
             {
-                _processStartupInterval = workerConfig.CountOptions.ProcessStartupInterval;
-                _restartWait = workerConfig.CountOptions.ProcessRestartInterval;
-                _shutdownTimeout = workerConfig.CountOptions.ProcessShutdownTimeout;
+                _processStartupInterval = workerConfig?.CountOptions?.ProcessStartupInterval ?? _defaultProcessStartupInterval;
+                _restartWait = workerConfig?.CountOptions.ProcessRestartInterval ?? _defaultProcessRestartInterval;
+                _shutdownTimeout = workerConfig?.CountOptions.ProcessShutdownTimeout ?? _defaultProcessShutdownInterval;
             }
             ErrorEventsThreshold = 3 * await _maxProcessCount.Value;
 
diff --git a/src/WebJobs.Script/Workers/Rpc/RpcWorkerConstants.cs b/src/WebJobs.Script/Workers/Rpc/RpcWorkerConstants.cs
index daa710cda9..b7a41b980b 100644
--- a/src/WebJobs.Script/Workers/Rpc/RpcWorkerConstants.cs
+++ b/src/WebJobs.Script/Workers/Rpc/RpcWorkerConstants.cs
@@ -93,5 +93,6 @@ public static class RpcWorkerConstants
         public const string RevertWorkerShutdownBehavior = "REVERT_WORKER_SHUTDOWN_BEHAVIOR";
         public const string ShutdownWebhostWorkerChannelsOnHostShutdown = "ShutdownWebhostWorkerChannelsOnHostShutdown";
         public const string ThrowOnMissingFunctionsWorkerRuntime = "THROW_ON_MISSING_FUNCTIONS_WORKER_RUNTIME";
+        public const string WorkerRuntimeStrictValidationEnabled = "WORKER_RUNTIME_STRICT_VALIDATION_ENABLED";
     }
 }
\ No newline at end of file
diff --git a/test/WebJobs.Script.Tests.Integration/WebHostEndToEnd/WebJobsStartupEndToEndTests.cs b/test/WebJobs.Script.Tests.Integration/WebHostEndToEnd/WebJobsStartupEndToEndTests.cs
index 699f911b9a..2f5ffd7054 100644
--- a/test/WebJobs.Script.Tests.Integration/WebHostEndToEnd/WebJobsStartupEndToEndTests.cs
+++ b/test/WebJobs.Script.Tests.Integration/WebHostEndToEnd/WebJobsStartupEndToEndTests.cs
@@ -3,6 +3,7 @@
 using System.Net;
 using System.Threading.Tasks;
 using Microsoft.Azure.WebJobs.Logging;
+using Microsoft.Azure.WebJobs.Script.Workers.Rpc;
 using Microsoft.Extensions.DependencyInjection;
 using Xunit;
 
@@ -45,6 +46,34 @@ public async Task ExternalStartup_Succeeds()
             }
         }
 
+        [Fact]
+        public async Task InProcAppsWorkWithDotnetIsolatedAsFunctionWorkerRuntimeValue()
+        {
+            // test uses an in-proc app, but we are setting "dotnet-isolated" as functions worker runtime value.
+            var fixture = new CSharpPrecompiledEndToEndTestFixture(_projectName, _envVars, functionWorkerRuntime: RpcWorkerConstants.DotNetIsolatedLanguageWorkerName);
+            try
+            {
+                await fixture.InitializeAsync();
+                var client = fixture.Host.HttpClient;
+
+                var response = await client.GetAsync($"api/Function1");
+
+                // The function does all the validation internally.
+                Assert.Equal(HttpStatusCode.OK, response.StatusCode);
+
+                const string expectedLogEntry =
+                    "The 'FUNCTIONS_WORKER_RUNTIME' is set to 'dotnet-isolated', " +
+                    "which does not match the worker runtime metadata found in the deployed function app artifacts. " +
+                    "The deployed artifacts are for 'dotnet'. See https://aka.ms/functions-invalid-worker-runtime " +
+                    "for more information. The application will continue to run, but may throw an exception in the future.";
+                Assert.Single(fixture.Host.GetScriptHostLogMessages(), p => p.FormattedMessage != null && p.FormattedMessage.EndsWith(expectedLogEntry));
+            }
+            finally
+            {
+                await fixture.DisposeAsync();
+            }
+        }
+
         [Fact]
         public async Task ExternalStartup_InvalidOverwrite_StopsHost()
         {
diff --git a/test/WebJobs.Script.Tests/Configuration/FunctionsHostingConfigOptionsTest.cs b/test/WebJobs.Script.Tests/Configuration/FunctionsHostingConfigOptionsTest.cs
index 20259e7612..55fcb3b80e 100644
--- a/test/WebJobs.Script.Tests/Configuration/FunctionsHostingConfigOptionsTest.cs
+++ b/test/WebJobs.Script.Tests/Configuration/FunctionsHostingConfigOptionsTest.cs
@@ -138,7 +138,8 @@ public void Property_Validation()
 
                 (nameof(FunctionsHostingConfigOptions.ThrowOnMissingFunctionsWorkerRuntime), "THROW_ON_MISSING_FUNCTIONS_WORKER_RUNTIME=1", true),
                 (nameof(FunctionsHostingConfigOptions.WorkerIndexingDisabledApps), "WORKER_INDEXING_DISABLED_APPS=teststring", "teststring"),
-                (nameof(FunctionsHostingConfigOptions.WorkerIndexingEnabled), "WORKER_INDEXING_ENABLED=1", true)
+                (nameof(FunctionsHostingConfigOptions.WorkerIndexingEnabled), "WORKER_INDEXING_ENABLED=1", true),
+                (nameof(FunctionsHostingConfigOptions.WorkerRuntimeStrictValidationEnabled), "WORKER_RUNTIME_STRICT_VALIDATION_ENABLED=1", true)
             };
 
             // use reflection to ensure that we have a test that uses every value exposed on FunctionsHostingConfigOptions