diff --git a/Src/CompareEngines/Wrap_DiffUtils.cpp b/Src/CompareEngines/Wrap_DiffUtils.cpp
index 4ab3b1a5b8b..88b7d636ef4 100644
--- a/Src/CompareEngines/Wrap_DiffUtils.cpp
+++ b/Src/CompareEngines/Wrap_DiffUtils.cpp
@@ -113,6 +113,7 @@ int DiffUtils::CompareFiles(DiffFileData* diffData)
 	if (script != nullptr)
 	{
 		const bool usefilters = m_pDiffWrapper->GetOptions().m_filterCommentsLines ||
+			m_pDiffWrapper->GetOptions().m_bIgnoreEofNewlinePresence ||
 			(m_pDiffWrapper->GetFilterList() && m_pDiffWrapper->GetFilterList()->HasRegExps()) ||
 			(m_pDiffWrapper->GetSubstitutionList() && m_pDiffWrapper->GetSubstitutionList()->HasRegExps());
 	
diff --git a/Src/CompareOptions.cpp b/Src/CompareOptions.cpp
index a218c442acb..5e06b9e39b6 100644
--- a/Src/CompareOptions.cpp
+++ b/Src/CompareOptions.cpp
@@ -49,6 +49,7 @@ void CompareOptions::SetFromDiffOptions(const DIFFOPTIONS &options)
 	m_bIgnoreCase = options.bIgnoreCase;
 	m_bIgnoreEOLDifference = options.bIgnoreEol;
 	m_bIgnoreNumbers = options.bIgnoreNumbers;
+	m_bIgnoreEofNewlinePresence = options.bIgnoreEofNewlinePresence;
 }
 
 /**
@@ -96,7 +97,6 @@ void DiffutilsOptions::SetFromDiffOptions(const DIFFOPTIONS & options)
 	CompareOptions::SetFromDiffOptions(options);
 	m_bCompletelyBlankOutIgnoredDiffereneces = options.bCompletelyBlankOutIgnoredChanges;
 	m_filterCommentsLines = options.bFilterCommentsLines;
-	m_bIgnoreEofNewlinePresence = options.bIgnoreEofNewlinePresence;
 	m_bIndentHeuristic = options.bIndentHeuristic;
 	switch (options.nDiffAlgorithm)
 	{
@@ -189,6 +189,7 @@ void DiffutilsOptions::GetAsDiffOptions(DIFFOPTIONS &options) const
 	options.bIgnoreEol = m_bIgnoreEOLDifference;
 	options.bIgnoreNumbers = m_bIgnoreNumbers;
 	options.nDiffAlgorithm = m_diffAlgorithm;
+	options.bIgnoreEofNewlinePresence = m_bIgnoreEofNewlinePresence;
 
 	switch (m_ignoreWhitespace)
 	{
diff --git a/Src/DiffWrapper.cpp b/Src/DiffWrapper.cpp
index 91e46e2afd1..ad590d4c6e3 100644
--- a/Src/DiffWrapper.cpp
+++ b/Src/DiffWrapper.cpp
@@ -339,6 +339,18 @@ static void ReplaceChars(std::string & str, const char* chars, const char *rep)
 	}
 }
 
+static void RemoveEOL(std::string& str)
+{
+	if (str.empty())
+		return;
+	if (str.size() >= 2 && str[str.size() - 2] == '\r' && str[str.size() - 1] == '\n')
+		str.erase(str.size() - 2, 2);
+	else if (str.back() == '\n')
+		str.pop_back();
+	else if (str.back() == '\r')
+		str.pop_back();
+}
+
 /**
  * @brief The main entry for post filtering.  Performs post-filtering, by setting comment blocks to trivial
  * @param [in, out]  thisob	Current change
@@ -447,6 +459,11 @@ int CDiffWrapper::PostFilter(PostFilterContext& ctxt, change* thisob, const file
 		Replace(lineDataRight, "\r\n", "\n");
 		Replace(lineDataRight, "\r", "\n");
 	}
+	if (thisob->link == nullptr && m_options.m_bIgnoreEofNewlinePresence && (file_data_ary[0].missing_newline || file_data_ary[1].missing_newline))
+	{
+		RemoveEOL(lineDataLeft);
+		RemoveEOL(lineDataRight);
+	}
 
 	// If both match after filtering, mark this diff hunk as trivial and return.
 	if (lineDataLeft == lineDataRight)