diff --git a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionDefinition.java b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionDefinition.java
index 5c73b720a0bc8..518411fce5fda 100644
--- a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionDefinition.java
+++ b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionDefinition.java
@@ -22,9 +22,11 @@ public static TransportVersionDefinition fromString(Path file, String contents,
 
         String idsLine = null;
         if (contents.isEmpty() == false) {
-            String[] lines = contents.split(System.lineSeparator());
+            // Regardless of whether windows newlines exist (they could be added by git), we split on line feed.
+            // All we care about skipping lines with the comment character, so the remaining \r won't matter
+            String[] lines = contents.split("\n");
             for (String line : lines) {
-                line = line.replaceAll("\\s+", "");
+                line = line.strip();
                 if (line.startsWith("#") == false) {
                     idsLine = line;
                     break;
diff --git a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionUpperBound.java b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionUpperBound.java
index af88aa646d790..b37d2ec3676ba 100644
--- a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionUpperBound.java
+++ b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/TransportVersionUpperBound.java
@@ -24,9 +24,11 @@ public static TransportVersionUpperBound fromString(Path file, String contents)
         String branch = filename.substring(slashIndex == -1 ? 0 : (slashIndex + 1), filename.length() - 4);
 
         String idsLine = null;
-        String[] lines = contents.split(System.lineSeparator());
+        // Regardless of whether windows newlines exist (they could be added by git), we split on line feed.
+        // All we care about skipping lines with the comment character, so the remaining \r won't matter
+        String[] lines = contents.split("\n");
         for (String line : lines) {
-            line = line.replaceAll("\\s+", "");
+            line = line.strip();
             if (line.startsWith("#") == false) {
                 idsLine = line;
                 break;