diff --git a/.ci/test_r_package.sh b/.ci/test_r_package.sh
index 275dea70b072..fca6b81466a3 100755
--- a/.ci/test_r_package.sh
+++ b/.ci/test_r_package.sh
@@ -219,30 +219,40 @@ if [[ $omp_working -ne 1 ]]; then
     exit -1
 fi
 
-# this check makes sure that CI builds of the CRAN package
+# this check makes sure that CI builds of the package
 # actually use MM_PREFETCH preprocessor definition
 if [[ $R_BUILD_TYPE == "cran" ]]; then
     mm_prefetch_working=$(
         cat $BUILD_LOG_FILE \
         | grep --count -E "checking whether MM_PREFETCH work.*yes"
     )
-    if [[ $mm_prefetch_working -ne 1 ]]; then
-        echo "MM_PREFETCH test was not passed, and should be when testing the CRAN package"
-        exit -1
-    fi
+else
+    mm_prefetch_working=$(
+        cat $BUILD_LOG_FILE \
+        | grep --count -E ".*Performing Test MM_PREFETCH - Success"
+    )
+fi
+if [[ $mm_prefetch_working -ne 1 ]]; then
+    echo "MM_PREFETCH test was not passed"
+    exit -1
 fi
 
-# this check makes sure that CI builds of the CRAN package
+# this check makes sure that CI builds of the package
 # actually use MM_MALLOC preprocessor definition
 if [[ $R_BUILD_TYPE == "cran" ]]; then
     mm_malloc_working=$(
         cat $BUILD_LOG_FILE \
         | grep --count -E "checking whether MM_MALLOC work.*yes"
     )
-    if [[ $mm_malloc_working -ne 1 ]]; then
-        echo "MM_MALLOC test was not passed, and should be when testing the CRAN package"
-        exit -1
-    fi
+else
+    mm_malloc_working=$(
+        cat $BUILD_LOG_FILE \
+        | grep --count -E ".*Performing Test MM_MALLOC - Success"
+    )
+fi
+if [[ $mm_malloc_working -ne 1 ]]; then
+    echo "MM_MALLOC test was not passed"
+    exit -1
 fi
 
 # this check makes sure that no "warning: unknown pragma ignored" logs
diff --git a/.ci/test_r_package_windows.ps1 b/.ci/test_r_package_windows.ps1
index 823be77b2161..3948db2ed357 100644
--- a/.ci/test_r_package_windows.ps1
+++ b/.ci/test_r_package_windows.ps1
@@ -232,22 +232,34 @@ if (($env:COMPILER -eq "MINGW") -and ($env:R_BUILD_TYPE -eq "cmake")) {
   }
 }
 
-# Checking that MM_PREFETCH preprocessor definition is actually used in CRAN builds.
+# Checking that MM_PREFETCH preprocessor definition is actually used in CI builds.
 if ($env:R_BUILD_TYPE -eq "cran") {
   $checks = Select-String -Path "${INSTALL_LOG_FILE_NAME}" -Pattern "checking whether MM_PREFETCH work.*yes"
-  if ($checks.Matches.length -eq 0) {
-    Write-Output "MM_PREFETCH preprocessor definition wasn't used. Check the build logs."
-    Check-Output $False
-  }
+  $checks_cnt = $checks.Matches.length
+} elseif ($env:TOOLCHAIN -ne "MSVC") {
+  $checks = Select-String -Path "${INSTALL_LOG_FILE_NAME}" -Pattern ".*Performing Test MM_PREFETCH - Success"
+  $checks_cnt = $checks.Matches.length
+} else {
+  $checks_cnt = 1
+}
+if ($checks_cnt -eq 0) {
+  Write-Output "MM_PREFETCH preprocessor definition wasn't used. Check the build logs."
+  Check-Output $False
 }
 
-# Checking that MM_MALLOC preprocessor definition is actually used in CRAN builds.
+# Checking that MM_MALLOC preprocessor definition is actually used in CI builds.
 if ($env:R_BUILD_TYPE -eq "cran") {
   $checks = Select-String -Path "${INSTALL_LOG_FILE_NAME}" -Pattern "checking whether MM_MALLOC work.*yes"
-  if ($checks.Matches.length -eq 0) {
-    Write-Output "MM_MALLOC preprocessor definition wasn't used. Check the build logs."
-    Check-Output $False
-  }
+  $checks_cnt = $checks.Matches.length
+} elseif ($env:TOOLCHAIN -ne "MSVC") {
+  $checks = Select-String -Path "${INSTALL_LOG_FILE_NAME}" -Pattern ".*Performing Test MM_MALLOC - Success"
+  $checks_cnt = $checks.Matches.length
+} else {
+  $checks_cnt = 1
+}
+if ($checks_cnt -eq 0) {
+  Write-Output "MM_MALLOC preprocessor definition wasn't used. Check the build logs."
+  Check-Output $False
 }
 
 # Checking that OpenMP is actually used in CMake builds.