diff --git a/clitests/CMakeLists.txt b/clitests/CMakeLists.txt
index 2e88c8d37..0dcf9a986 100644
--- a/clitests/CMakeLists.txt
+++ b/clitests/CMakeLists.txt
@@ -250,12 +250,18 @@ set(CASELIST
     tests/encode/encode_error_normal_mode.json
 )
 
-set(CASE_REGEN_GOLDEN_COMMANDS)
+set(CASE_REGEN_GOLDEN_OUTPUTS)
 
 if(NOT DEFINED KTX_TOOLS_PATH)
     message(FATAL_ERROR "KTX_TOOLS_PATH not defined")
 endif()
 
+if(MSVC)
+    set(CLITEST_ARGS "--msvc")
+else()
+    set(CLITEST_ARGS "")
+endif()
+
 foreach(CASE_FILE ${CASELIST})
     get_filename_component(CASE_DIR ${CASE_FILE} DIRECTORY)
     get_filename_component(CASE_NAME ${CASE_FILE} NAME_WE)
@@ -263,14 +269,16 @@ foreach(CASE_FILE ${CASELIST})
     string(REPLACE "/" "." CASE_GROUP "${CASE_TRIMMED_DIR}")
     set(FULL_CASE_NAME "${CASE_GROUP}${CASE_NAME}")
 
-    list(APPEND CASE_REGEN_GOLDEN_COMMANDS
-        COMMAND ${PYTHON_EXECUTABLE} clitest.py ${CASE_FILE} --executable-path ${KTX_TOOLS_PATH} --regen-golden)
+    list(APPEND CASE_REGEN_GOLDEN_OUTPUTS ${CASE_FILE})
+    add_custom_command(
+        OUTPUT ${CASE_FILE}
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} clitest.py ${CASE_FILE} ${CLITEST_ARGS} --executable-path ${KTX_TOOLS_PATH} --regen-golden)
 
     add_test(NAME ${FULL_CASE_NAME}
-        COMMAND ${PYTHON_EXECUTABLE} clitest.py ${CASE_FILE} --executable-path ${KTX_TOOLS_PATH}
+        COMMAND ${PYTHON_EXECUTABLE} clitest.py ${CASE_FILE} ${CLITEST_ARGS} --executable-path ${KTX_TOOLS_PATH}
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 endforeach()
 
 add_custom_target(clitests_regen_golden
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    ${CASE_REGEN_GOLDEN_COMMANDS})
+    DEPENDS ${CASE_REGEN_GOLDEN_OUTPUTS})
diff --git a/clitests/clitest.py b/clitests/clitest.py
index 8cd4e813b..19a5676a6 100644
--- a/clitests/clitest.py
+++ b/clitests/clitest.py
@@ -55,6 +55,8 @@ def cmdArgs(self):
                         help='Regenerate reference files')
     parser.add_argument('-e', '--executable-path', action='store', required=True,
                         help='Path to use for the executed command')
+    parser.add_argument('--msvc', action='store_true',
+                        help='Indicates that test runs against MSVC build')
 
     cli_args, unknown_args = parser.parse_known_args()
 
@@ -108,7 +110,8 @@ def cmdArgs(self):
 
     # Execute subcases
 
-    print(f"Executing test case '{cli_args.json_test_file}'...")
+    if not cli_args.regen_golden:
+        print(f"Executing test case '{cli_args.json_test_file}'...")
 
     failed = False
     messages = []
@@ -116,6 +119,8 @@ def cmdArgs(self):
     subcases_skipped = 0
     subcases_failed = 0
 
+    ref_not_updated = {}
+
     for subcase_index, subcase in enumerate(subcases):
         skip_subcase = False
 
@@ -134,7 +139,8 @@ def cmdArgs(self):
         subcase_failed = False
         subcase_messages = []
 
-        messages.append(f"  {ctx.eval(testcase['command'])}")
+        if not cli_args.regen_golden:
+            messages.append(f"  {ctx.eval(testcase['command'])}")
 
         # Run command
 
@@ -212,8 +218,7 @@ def cmdArgs(self):
                         old_output_ref_contains_regex = bool(re.findall(r'`.*`', old_output_ref))
 
                     if old_output_ref_contains_regex:
-                        subcase_messages.append(f"Warning: reference file '{output_ref_filename}' was not updated as it contains a regex")
-                        subcase_failed = True
+                        ref_not_updated[output_ref_filename] = f"NOTE: reference file '{output_ref_filename}' was not updated as it contains a regex"
                     else:
                         os.makedirs(os.path.dirname(output_ref_filename), exist_ok=True)
                         output_ref_file = open(output_ref_filename, 'w+', newline='\n', encoding='utf-8')
@@ -253,7 +258,10 @@ def cmdArgs(self):
                 if not cmd_failed and cli_args.regen_golden:
                     os.makedirs(os.path.dirname(output_ref), exist_ok=True)
                     if os.path.isfile(output_cur):
-                        shutil.copyfile(output_cur, output_ref)
+                        if cli_args.msvc and 'allowOutputMismatchOnMSVC' in testcase:
+                            ref_not_updated[output_ref] = f"NOTE: reference file '{output_ref}' was not updated on MSVC build as it has MSVC output mismatches allowed"
+                        else:
+                            shutil.copyfile(output_cur, output_ref)
                     else:
                         subcase_failed = True
                         subcase_messages.append(f"stdout:\n{output['stdout']}")
@@ -270,8 +278,11 @@ def cmdArgs(self):
                     files_found = False
 
                 if files_found and not filecmp.cmp(output_cur, output_ref, shallow=False):
-                    subcase_messages.append(f"Mismatch between output file '{output_cur}' and reference file '{output_ref}'")
-                    subcase_failed = True
+                    if cli_args.msvc and 'allowOutputMismatchOnMSVC' in testcase:
+                        messages.append(f"    WARNING: allowed mismatch on MSVC build between output file '{output_cur}' and reference file '{output_ref}'")
+                    else:
+                        subcase_messages.append(f"Mismatch between output file '{output_cur}' and reference file '{output_ref}'")
+                        subcase_failed = True
 
 
         # Handle subcase failure
@@ -293,11 +304,15 @@ def cmdArgs(self):
     for message in messages:
         print(message)
 
-    print("Subcase summary:")
-    print(f"  Passed:  {subcases_passed}")
-    print(f"  Skipped: {subcases_skipped}")
-    print(f"  Failed:  {subcases_failed}")
-    print(f"  Total:   {len(subcases)}")
+    for ref in ref_not_updated:
+        print(ref_not_updated[ref])
+
+    if not cli_args.regen_golden:
+        print("Subcase summary:")
+        print(f"  Passed:  {subcases_passed}")
+        print(f"  Skipped: {subcases_skipped}")
+        print(f"  Failed:  {subcases_failed}")
+        print(f"  Total:   {len(subcases)}")
 
-    if failed and not cli_args.regen_golden:
+    if failed:
         exit(1)
diff --git a/clitests/tests/create/encode_blze.json b/clitests/tests/create/encode_blze.json
index 83564362b..8bf6a9426 100644
--- a/clitests/tests/create/encode_blze.json
+++ b/clitests/tests/create/encode_blze.json
@@ -2,6 +2,7 @@
     "description": "Test create with default behavior of BasisLZ encoding.",
     "command": "ktx create --raw --format ${subcase} --width 8 --height 8 --testrun --threads 1 --encode basis-lz input/raw/raw_${subcase}_2D_8x8.raw output/create/encode_blze/output_${subcase}.ktx2",
     "status": 0,
+    "allowOutputMismatchOnMSVC": "BasisLZ compression relies on undefined order of std::unordered_map containers.",
     "outputs": {
         "output/create/encode_blze/output_${subcase}.ktx2": "golden/create/encode_blze/output_${subcase}.ktx2"
     },
diff --git a/clitests/tests/create/encode_blze_params.json b/clitests/tests/create/encode_blze_params.json
index e74fce217..2b1a9c133 100644
--- a/clitests/tests/create/encode_blze_params.json
+++ b/clitests/tests/create/encode_blze_params.json
@@ -2,6 +2,7 @@
     "description": "Test create with BasisLZ encoding with various parameter combinations.",
     "command": "ktx create --raw --format ${subcase} --width 8 --height 8 --testrun --threads 1 --encode basis-lz ${select[args]} input/raw/raw_${subcase}_2D_8x8.raw output/create/encode_blze_params/output_${subcase}_${select[id]}.ktx2",
     "status": 0,
+    "allowOutputMismatchOnMSVC": "BasisLZ compression relies on undefined order of std::unordered_map containers.",
     "outputs": {
         "output/create/encode_blze_params/output_${subcase}_${select[id]}.ktx2": "golden/create/encode_blze_params/output_${subcase}_${select[id]}.ktx2"
     },
diff --git a/clitests/tests/encode/encode_blze.json b/clitests/tests/encode/encode_blze.json
index 8ee2f30c5..13c70cff4 100644
--- a/clitests/tests/encode/encode_blze.json
+++ b/clitests/tests/encode/encode_blze.json
@@ -2,6 +2,7 @@
     "description": "Test default behavior of BasisLZ encoding.",
     "command": "ktx encode --testrun --threads 1 --codec basis-lz input/valid/valid_${subcase}.ktx2 output/encode/encode_blze/output_${subcase}.ktx2",
     "status": 0,
+    "allowOutputMismatchOnMSVC": "BasisLZ compression relies on undefined order of std::unordered_map containers.",
     "outputs": {
         "output/encode/encode_blze/output_${subcase}.ktx2": "golden/encode/encode_blze/output_${subcase}.ktx2"
     },
diff --git a/clitests/tests/encode/encode_blze_params.json b/clitests/tests/encode/encode_blze_params.json
index 590f13740..edd746ff5 100644
--- a/clitests/tests/encode/encode_blze_params.json
+++ b/clitests/tests/encode/encode_blze_params.json
@@ -2,6 +2,7 @@
     "description": "Test BasisLZ encoding with various parameter combinations.",
     "command": "ktx encode --testrun --threads 1 --codec basis-lz ${select[args]} input/encode/large_${subcase}_ZSTD.ktx2 output/encode/encode_blze_params/output_${subcase}_${select[id]}.ktx2",
     "status": 0,
+    "allowOutputMismatchOnMSVC": "BasisLZ compression relies on undefined order of std::unordered_map containers.",
     "outputs": {
         "output/encode/encode_blze_params/output_${subcase}_${select[id]}.ktx2": "golden/encode/encode_blze_params/output_${subcase}_${select[id]}.ktx2"
     },