diff --git a/.autover/changes/49c69f86-aa08-45d2-ba6b-70117f5f1d1d.json b/.autover/changes/49c69f86-aa08-45d2-ba6b-70117f5f1d1d.json
new file mode 100644
index 0000000..c92ceed
--- /dev/null
+++ b/.autover/changes/49c69f86-aa08-45d2-ba6b-70117f5f1d1d.json
@@ -0,0 +1,11 @@
+{
+  "Projects": [
+    {
+      "Name": "Amazon.ElasticBeanstalk.Tools",
+      "Type": "Patch",
+      "ChangelogMessages": [
+        "Fixed an ElasticBeanstalk deployment issue for Linux platform where Procfile was sometimes being generated with incorrect entrypoint when multiple runtimeconfig.json files were present."
+      ]
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/Amazon.ElasticBeanstalk.Tools/EBUtilities.cs b/src/Amazon.ElasticBeanstalk.Tools/EBUtilities.cs
index 964397b..0aa71b9 100644
--- a/src/Amazon.ElasticBeanstalk.Tools/EBUtilities.cs
+++ b/src/Amazon.ElasticBeanstalk.Tools/EBUtilities.cs
@@ -3,7 +3,6 @@
 using System.Globalization;
 using System.IO;
 using System.Linq;
-using System.Runtime.CompilerServices;
 using Amazon.Common.DotNetCli.Tools;
 using Amazon.ElasticBeanstalk.Model;
 using Amazon.ElasticBeanstalk.Tools.Commands;
@@ -108,26 +107,24 @@ public static bool IsLoadBalancedEnvironmentType(string environmentType)
             return string.Equals(environmentType, EBConstants.ENVIRONMENT_TYPE_LOADBALANCED, StringComparison.OrdinalIgnoreCase);
         }
 
-
         public static void SetupPackageForLinux(IToolLogger logger, EBBaseCommand command, DeployEnvironmentProperties options, string publishLocation, string reverseProxy, int? applicationPort)
         {
             // Setup Procfile
             var procfilePath = Path.Combine(publishLocation, "Procfile");
 
-            if(File.Exists(procfilePath))
+            if (File.Exists(procfilePath))
             {
                 logger?.WriteLine("Found existing Procfile file found and using that for deployment");
                 return;
             }
 
             logger?.WriteLine("Writing Procfile for deployment bundle");
-
-            var runtimeConfigFilePath = Directory.GetFiles(publishLocation, "*.runtimeconfig.json").FirstOrDefault();
+            string runtimeConfigFilePath = GetRuntimeConfigFilePath(publishLocation);
             var runtimeConfigFileName = Path.GetFileName(runtimeConfigFilePath);
             var executingAssembly = runtimeConfigFileName.Substring(0, runtimeConfigFileName.Length - "runtimeconfig.json".Length - 1);
 
             string webCommandLine;
-            if(IsSelfContainedPublish(runtimeConfigFilePath))
+            if (IsSelfContainedPublish(runtimeConfigFilePath))
             {
                 webCommandLine = $"./{executingAssembly}";
             }
@@ -136,7 +133,7 @@ public static void SetupPackageForLinux(IToolLogger logger, EBBaseCommand comman
                 webCommandLine = $"dotnet exec ./{executingAssembly}.dll";
             }
 
-            if(string.Equals(reverseProxy, EBConstants.PROXY_SERVER_NONE, StringComparison.InvariantCulture))
+            if (string.Equals(reverseProxy, EBConstants.PROXY_SERVER_NONE, StringComparison.InvariantCulture))
             {
                 logger?.WriteLine("... Proxy server disabled, configuring Kestrel to listen to traffic from all hosts");
                 var port = applicationPort.HasValue ? applicationPort.Value : EBConstants.DEFAULT_APPLICATION_PORT;
@@ -175,5 +172,65 @@ public static string FindExistingValue(this List<ConfigurationOptionSetting> set
             var setting = settings?.FirstOrDefault(x => string.Equals(x.Namespace, ns, StringComparison.InvariantCulture) && string.Equals(x.OptionName, name, StringComparison.InvariantCulture));
             return setting?.Value;
         }
+
+        private static string GetRuntimeConfigFilePath(string publishLocation)
+        {
+            var runtimeConfigFiles = Directory.GetFiles(publishLocation, "*.runtimeconfig.json");
+
+            // Handle case where application could have multiple runtimeconfig.json files in publish location.
+            if (runtimeConfigFiles.Length > 1)
+            {
+                foreach (var file in runtimeConfigFiles)
+                {
+                    var fileContent = File.ReadAllText(file);
+
+                    JsonData root = JsonMapper.ToObject(fileContent);
+                    JsonData runtimeOptions = root["runtimeOptions"] as JsonData;
+                    if (runtimeOptions == null)
+                    {
+                        continue;
+                    }
+
+                    // runtimeOptions node can contain framework or frameworks (refer https://github.com/dotnet/sdk/blob/main/documentation/specs/runtime-configuration-file.md#runtimeoptions-section-runtimeconfigjson).
+                    var frameworkNode = runtimeOptions["framework"];
+                    var frameworksNode = runtimeOptions["frameworks"];
+
+                    if (IsAspNetFramework(frameworkNode))
+                    {
+                        return file;
+                    }
+
+                    if (frameworksNode != null && frameworksNode.Count > 0)
+                    {
+                        foreach (var framework in frameworksNode)
+                        {
+                            var tempNode = framework as JsonData;
+                            if (IsAspNetFramework(tempNode))
+                            {
+                                return file;
+                            }
+                        }
+                    }
+                }
+            }
+
+            return Directory.GetFiles(publishLocation, "*.runtimeconfig.json").FirstOrDefault();
+        }
+
+        private static bool IsAspNetFramework(JsonData frameworkNode)
+        {
+            if (frameworkNode != null)
+            {
+                var name = frameworkNode["name"];
+
+                if (name != null)
+                {
+                    string frameworkName = (string)name;
+                    return !string.IsNullOrEmpty(frameworkName) && frameworkName.StartsWith("Microsoft.AspNetCore");
+                }
+            }
+
+            return false;
+        }
     }
 }