diff --git a/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java
index 0e3b8bf73..bba25629b 100644
--- a/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java
+++ b/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java
@@ -55,7 +55,8 @@ public void testCompareModified() throws IOException, OWLOntologyCreationExcepti
     assertFalse(actual);
     String expected =
         IOUtils.toString(
-            this.getClass().getResourceAsStream("/simple1.diff"), Charset.defaultCharset());
+                this.getClass().getResourceAsStream("/simple1.diff"), Charset.defaultCharset())
+            .replaceAll("\r\n", "\n");
     assertEquals(expected, writer.toString());
   }
 
@@ -77,7 +78,8 @@ public void testCompareModifiedWithLabels() throws IOException {
     assertFalse(actual);
     String expected =
         IOUtils.toString(
-            this.getClass().getResourceAsStream("/simple.diff"), Charset.defaultCharset());
+                this.getClass().getResourceAsStream("/simple.diff"), Charset.defaultCharset())
+            .replaceAll("\r\n", "\n");
     assertEquals(expected, writer.toString());
   }
 
diff --git a/robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java b/robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java
index a70110995..8ecf95131 100644
--- a/robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java
+++ b/robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java
@@ -53,7 +53,7 @@ public void testAddPrefixes() throws IOException {
     ioh.addPrefixes(context);
 
     // Get the context back from IOHelper
-    String outputContext = ioh.getContextString();
+    String outputContext = ioh.getContextString().replaceAll("\r\n", "\n");
     assertEquals(inputContext, outputContext);
   }
 
@@ -166,7 +166,7 @@ public void testPrefixHandling() throws IOException {
 
     String json =
         "{\n" + "  \"@context\" : {\n" + "    \"foo\" : \"http://example.com#\"\n" + "  }\n" + "}";
-    assertEquals("Check JSON-LD", json, ioh.getContextString());
+    assertEquals("Check JSON-LD", json, ioh.getContextString().replaceAll("\r\n", "\n"));
 
     ioh.addPrefix("bar: http://example.com#");
     expected.put("bar", "http://example.com#");
diff --git a/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
index 0f6d9a760..50803c7b0 100644
--- a/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
+++ b/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
@@ -48,12 +48,14 @@ private void testReportProducesCorrectOutput(String extension) throws Exception
           File.createTempFile("1016-report-json-failure-output", "." + extension);
       ReportOperation.report(ontology, iohelper, outputFile.toString(), Collections.emptyMap());
       final String output =
-          IOUtils.toString(new FileInputStream(outputFile), Charset.defaultCharset()).trim();
+          IOUtils.toString(new FileInputStream(outputFile), Charset.defaultCharset())
+              .trim()
+              .replaceAll("\r\n", "\n");
       final InputStream expected =
           getClass().getResourceAsStream("/1016-report-json-failure/output." + extension);
       assert expected != null;
       final String expectedOutput =
-          IOUtils.toString(expected, StandardCharsets.UTF_8.name()).trim();
+          IOUtils.toString(expected, StandardCharsets.UTF_8.name()).trim().replaceAll("\r\n", "\n");
       Assert.assertEquals(expectedOutput, output);
     } catch (YAMLException e) {
       e.printStackTrace();