diff --git a/tools/buildmgr/cbuildgen/src/CMakeListsGenerator.cpp b/tools/buildmgr/cbuildgen/src/CMakeListsGenerator.cpp
index 5696647e3..0674c3683 100644
--- a/tools/buildmgr/cbuildgen/src/CMakeListsGenerator.cpp
+++ b/tools/buildmgr/cbuildgen/src/CMakeListsGenerator.cpp
@@ -65,12 +65,12 @@ bool CMakeListsGenerator::GenBuildCMakeLists(void) {
     cmakelists << EOL << "set(LD_FLAGS_LIBRARIES \"" << CbuildUtils::EscapeQuotes(m_linkerLibsGlobal) << "\")";
   }
 
+  const string linkerExt = fs::path(m_linkerScript).extension().generic_string();
   if (!m_linkerScript.empty()) {
     cmakelists << EOL << "set(LD_SCRIPT \"" << m_linkerScript << "\")";
     if (!m_linkerRegionsFile.empty()) {
       cmakelists << EOL << "set(LD_REGIONS \"" << m_linkerRegionsFile << "\")";
     }
-    const string linkerExt = fs::path(m_linkerScript).extension().generic_string();
     if ((linkerExt == SRCPPEXT) || !m_linkerRegionsFile.empty() || !m_linkerPreProcessorDefines.empty()) {
       string absLinkerScript = fs::path(m_linkerScript).filename().generic_string();
       RteFsUtils::NormalizePath(absLinkerScript, m_intdir);
@@ -508,7 +508,7 @@ bool CMakeListsGenerator::GenBuildCMakeLists(void) {
   cmakelists << "_LINK_FLAGS \"${LD_CPU}";
   if (!m_linkerScript.empty() && !lib_output) {
     cmakelists << " ${_LS}\\\"${LD_SCRIPT";
-    if (!m_linkerRegionsFile.empty() || !m_linkerPreProcessorDefines.empty()) {
+    if ((linkerExt == SRCPPEXT) || !m_linkerRegionsFile.empty() || !m_linkerPreProcessorDefines.empty()) {
       cmakelists << "_PP";
     }
     cmakelists << "}\\\"";
@@ -706,7 +706,7 @@ bool CMakeListsGenerator::GenBuildCMakeLists(void) {
   }
 
   // Linker script pre-processing
-  if (!m_linkerScript.empty() && !lib_output && (!m_linkerRegionsFile.empty() || !m_linkerPreProcessorDefines.empty())) {
+  if (!m_linkerScript.empty() && !lib_output && ((linkerExt == SRCPPEXT) || !m_linkerRegionsFile.empty() || !m_linkerPreProcessorDefines.empty())) {
     cmakelists << EOL << "# Linker script pre-processing" << EOL << EOL;
     cmakelists << "add_custom_command(TARGET ${TARGET} PRE_LINK COMMAND ${CPP} ARGS ${CPP_ARGS_LD_SCRIPT} BYPRODUCTS ${LD_SCRIPT_PP})" << EOL;
   }
diff --git a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/CMakeLists.txt.ref b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/CMakeLists.txt.ref
index c1f714b1d..67d4e16ec 100644
--- a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/CMakeLists.txt.ref
+++ b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/CMakeLists.txt.ref
@@ -20,11 +20,6 @@ set(LD_FLAGS_GLOBAL "--entry=Reset_Handler --specs=nosys.specs -mcpu=cortex-m3 -
 set(LD_SCRIPT "C:/sandbox/devtools/build/TestOutput/TestData/Examples/GCC/LinkerPreProcessing/RTE/Device/ARMCM3/gcc_arm.ld.src")
 set(LD_SCRIPT_PP "C:/sandbox/devtools/build/TestOutput/TestData/Examples/GCC/LinkerPreProcessing/IntDir/gcc_arm.ld")
 
-set(LD_SCRIPT_PP_DEFINES
-  LD_PP_DEF0
-  LD_PP_DEF1=3U
-)
-
 set(DEFINES
   ARMCM3
   _RTE_
diff --git a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/MyProject.cprj b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/MyProject.cprj
index 5e9cd1c22..a0a6c3682 100644
--- a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/MyProject.cprj
+++ b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/MyProject.cprj
@@ -18,9 +18,7 @@
 
   <target Ddsp="NO_DSP" Dendian="Little-endian" Dfpu="NO_FPU" Dmve="NO_MVE" Dname="ARMCM3" Dsecure="Non-secure" Dtz="NO_TZ" Dvendor="ARM:82">
     <output name="MyProject"/>
-    <ldflags add="--entry=Reset_Handler --specs=nosys.specs -mcpu=cortex-m3 -mthumb" compiler="GCC" file="./RTE/Device/ARMCM3/gcc_arm.ld.src">
-      <defines>LD_PP_DEF0;LD_PP_DEF1=3U</defines>
-    </ldflags>
+    <ldflags add="--entry=Reset_Handler --specs=nosys.specs -mcpu=cortex-m3 -mthumb" compiler="GCC" file="./RTE/Device/ARMCM3/gcc_arm.ld.src"/>
     <cflags add="-O -Wall -gdwarf-2 -mapcs-frame -mthumb" compiler="GCC"/>
   </target>
 
diff --git a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/RTE/Device/ARMCM3/gcc_arm.ld.src b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/RTE/Device/ARMCM3/gcc_arm.ld.src
index e17b08d01..ad7cae88f 100644
--- a/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/RTE/Device/ARMCM3/gcc_arm.ld.src
+++ b/tools/buildmgr/test/testinput/Examples/GCC/LinkerPreProcessingSrcFile/RTE/Device/ARMCM3/gcc_arm.ld.src
@@ -43,19 +43,6 @@
 #define __STACK_SIZE        0x00000200
 #define __HEAP_SIZE         0x00000C00
 
-/* ----------------------------------------------------------------------------
- Test case 'defines' check
- *----------------------------------------------------------------------------*/
-#ifndef LD_PP_DEF0
-  #error "LD_PP_DEF0 was not defined"
-#endif
-#ifndef LD_PP_DEF1
-  #error "LD_PP_DEF1 was not defined"
-#endif
-#if (LD_PP_DEF1 != 3U)
-  #error "LD_PP_DEF1 is not equal to 3U"
-#endif
-
 /* ----------------------------------------------------------------------------
   Stack seal size definition
  *----------------------------------------------------------------------------*/
diff --git a/tools/projmgr/src/ProjMgrWorker.cpp b/tools/projmgr/src/ProjMgrWorker.cpp
index d12b16d31..d933415ff 100644
--- a/tools/projmgr/src/ProjMgrWorker.cpp
+++ b/tools/projmgr/src/ProjMgrWorker.cpp
@@ -1869,6 +1869,7 @@ bool ProjMgrWorker::ProcessConfigFiles(ContextItem& context) {
   if (context.linker.autoGen) {
     if (!context.linker.script.empty()) {
       ProjMgrLogger::Warn("conflict: automatic linker script generation overrules specified script '" + context.linker.script + "'");
+      context.linker.script.clear();
     }
   } else if (context.linker.script.empty() && context.linker.regions.empty() && context.linker.defines.empty()) {
     const auto& groups = context.rteActiveTarget->GetProjectGroups();