diff --git a/keepsorted/line_group.go b/keepsorted/line_group.go
index a637de8..d45a740 100644
--- a/keepsorted/line_group.go
+++ b/keepsorted/line_group.go
@@ -119,7 +119,7 @@ func groupLines(lines []string, metadata blockMetadata) []*lineGroup {
 	// Returns another boolean indicating whether the group should be ending
 	// after that line if so.
 	shouldAddToRegexDelimitedGroup := func(l string) (addToGroup bool, finishGroupAfter bool) {
-        if metadata.opts.GroupStartRegex != nil {
+		if metadata.opts.GroupStartRegex != nil {
 			// For GroupStartRegex, all non-regex-matching lines should be
 			// part of the group including prior lines.
 			return !matchesAnyRegex(l, metadata.opts.GroupStartRegex), false
@@ -349,7 +349,7 @@ func (cb *codeBlock) append(s string, opts blockOptions) {
 		cb.braceCounts = make(map[string]int)
 	}
 
-	// TODO(jfalgout): Does this need to handle runes more correctly?
+	// TODO: jfaer - Does this need to handle runes more correctly?
 	for i := 0; i < len(s); {
 		if cb.expectedQuote == "" {
 			// We do not appear to be inside a string literal.
@@ -419,8 +419,18 @@ func (lg *lineGroup) commentOnly() bool {
 }
 
 func (lg *lineGroup) regexTokens() []regexToken {
-	// TODO: jfaer - Should we match regexes on the original content?
-	regexMatches := lg.opts.matchRegexes(lg.internalJoinedLines())
+	var regexMatches []regexMatch
+	if len(lg.opts.ByRegex) == 0 {
+		// We apply other options on top of what the regex extracts, but if the user
+		// didn't set by_regex, we should fall back to the behavior they would've
+		// expected before we started supporting by_regex.
+		// Namely: We would apply the other options on top of the
+		// internalJoinedLines() instead of the raw content.
+		regexMatches = []regexMatch{{lg.internalJoinedLines()}}
+	} else {
+		regexMatches = lg.opts.matchRegexes(lg.regexJoinedLines())
+	}
+
 	ret := make([]regexToken, len(regexMatches))
 	if lg.access.regexTokens == nil {
 		lg.access.regexTokens = make([]regexTokenAccessRecorder, len(regexMatches))
@@ -453,8 +463,15 @@ func (lg *lineGroup) regexTokens() []regexToken {
 	return ret
 }
 
-// internalJoinedLines calculates the same thing as joinedLines, except it
-// doesn't record that it was used in the accessRecorder.
+// internalJoinedLines attempts to concatenate all of this lineGroup's content
+// the same way a reasonable human might.
+//
+// If the previous line ends with a "word" character and the current line starts
+// with a "word" character, the two lines will be separated by a space.
+// Otherwise, the lines are concatenated without any separation.
+//
+// Unlike joinedLines, this method does not record that it was used in the
+// accessRecorder.
 func (lg *lineGroup) internalJoinedLines() string {
 	if len(lg.lines) == 0 {
 		return ""
@@ -475,6 +492,25 @@ func (lg *lineGroup) internalJoinedLines() string {
 	return s.String()
 }
 
+// regexJoinedLines concatenates all of this lineGroup's content in a way that's
+// friendlier to regexes than internalJoinedLines.
+//
+// Primarily, this method still strips leading whitespace but it uses a real
+// newline character to separate lines instead of the "word" character logic of
+// internalJoinedLines.
+func (lg *lineGroup) regexJoinedLines() string {
+	if len(lg.lines) == 0 {
+		return ""
+	}
+	lines := make([]string, len(lg.lines))
+	for i, l := range lg.lines {
+		lines[i] = strings.TrimLeftFunc(l, unicode.IsSpace)
+	}
+	return strings.Join(lines, "\n")
+}
+
+// joinedLines returns internalJoinedLines and records that it was called in the
+// accessRecorder.
 func (lg *lineGroup) joinedLines() string {
 	lg.access.joinedLines = true
 	return lg.internalJoinedLines()
diff --git a/keepsorted/options_parser.go b/keepsorted/options_parser.go
index 4943842..2273631 100644
--- a/keepsorted/options_parser.go
+++ b/keepsorted/options_parser.go
@@ -125,7 +125,7 @@ func (p *parser) popIntOrBool() (IntOrBool, error) {
 func (ar *ByRegexOption) UnmarshalYAML(node *yaml.Node) error {
 	switch node.Tag {
 	case "!!str":
-		pat, err := regexp.Compile(node.Value)
+		pat, err := compileByRegex(node.Value)
 		if err != nil {
 			return err
 		}
@@ -141,7 +141,7 @@ func (ar *ByRegexOption) UnmarshalYAML(node *yaml.Node) error {
 			return fmt.Errorf("by_regex map item must have exactly one key-value pair, but got %d", len(m))
 		}
 		for pattern, template := range m {
-			pat, err := regexp.Compile(pattern)
+			pat, err := compileByRegex(pattern)
 			if err != nil {
 				return fmt.Errorf("invalid regex pattern %q: %w", pattern, err)
 			}
@@ -191,7 +191,7 @@ func (p *parser) popList() ([]string, error) {
 
 func (p *parser) popByRegexOption() ([]ByRegexOption, error) {
 	return popListValue(p, func(s string) (ByRegexOption, error) {
-		pat, err := regexp.Compile(s)
+		pat, err := compileByRegex(s)
 		return ByRegexOption{Pattern: pat}, err
 	})
 }
@@ -321,3 +321,14 @@ func (iter *runeIter) pop() (rune, bool) {
 	}
 	return ch, ok
 }
+
+func compileByRegex(re string) (*regexp.Regexp, error) {
+	if !strings.HasPrefix(re, "(?s)") && !strings.HasPrefix(re, "(?-s)") {
+		// The initial version of by_regex ran on top of lineGroup.joinedLines. This
+		// meant that users wrote regexes that didn't need to handle newlines.
+		// To minimize disruption, we automatically set dotall flag so that their
+		// regexes might still work after we start using real newlines.
+		re = "(?s)" + re
+	}
+	return regexp.Compile(re)
+}
diff --git a/keepsorted/options_parser_test.go b/keepsorted/options_parser_test.go
index 284cab5..051a9a1 100644
--- a/keepsorted/options_parser_test.go
+++ b/keepsorted/options_parser_test.go
@@ -218,7 +218,7 @@ func TestPopValue(t *testing.T) {
 			name: "Regex",
 
 			input: ".*",
-			want:  []ByRegexOption{{regexp.MustCompile(".*"), nil}},
+			want:  []ByRegexOption{{regexp.MustCompile("(?s).*"), nil}},
 		},
 		{
 			name: "MultipleRegex",
@@ -226,9 +226,9 @@ func TestPopValue(t *testing.T) {
 			input:         `[.*, abcd, '(?:efgh)ijkl']`,
 			allowYAMLList: true,
 			want: []ByRegexOption{
-				{regexp.MustCompile(".*"), nil},
-				{regexp.MustCompile("abcd"), nil},
-				{regexp.MustCompile("(?:efgh)ijkl"), nil},
+				{regexp.MustCompile("(?s).*"), nil},
+				{regexp.MustCompile("(?s)abcd"), nil},
+				{regexp.MustCompile("(?s)(?:efgh)ijkl"), nil},
 			},
 		},
 		{
@@ -237,10 +237,10 @@ func TestPopValue(t *testing.T) {
 			input:         `[.*, Mon: 0, '\b(\d{2})/(\d{2})/(\d{4})\b': '${3}-${1}-${2}', "0: 1": 2]`,
 			allowYAMLList: true,
 			want: []ByRegexOption{
-				{regexp.MustCompile(".*"), nil},
-				{regexp.MustCompile("Mon"), &([]string{"0"})[0]},
-				{regexp.MustCompile(`\b(\d{2})/(\d{2})/(\d{4})\b`), &([]string{"${3}-${1}-${2}"})[0]},
-				{regexp.MustCompile(`0: 1`), &([]string{"2"})[0]},
+				{regexp.MustCompile("(?s).*"), nil},
+				{regexp.MustCompile("(?s)Mon"), &([]string{"0"})[0]},
+				{regexp.MustCompile(`(?s)\b(\d{2})/(\d{2})/(\d{4})\b`), &([]string{"${3}-${1}-${2}"})[0]},
+				{regexp.MustCompile(`(?s)0: 1`), &([]string{"2"})[0]},
 			},
 		},
 		{
diff --git a/keepsorted/options_test.go b/keepsorted/options_test.go
index bdcfa56..8ca18d7 100644
--- a/keepsorted/options_test.go
+++ b/keepsorted/options_test.go
@@ -194,7 +194,8 @@ func TestBlockOptions(t *testing.T) {
 			want: blockOptions{
 				AllowYAMLLists: true,
 				ByRegex: []ByRegexOption{
-					{regexp.MustCompile("(?:abcd)"), nil}, {regexp.MustCompile("efg.*"), nil},
+					{regexp.MustCompile("(?s)(?:abcd)"), nil},
+					{regexp.MustCompile("(?s)efg.*"), nil},
 				},
 			},
 		},
@@ -206,8 +207,8 @@ func TestBlockOptions(t *testing.T) {
 			want: blockOptions{
 				AllowYAMLLists: true,
 				ByRegex: []ByRegexOption{
-					{Pattern: regexp.MustCompile(`.*`)},
-					{Pattern: regexp.MustCompile(`\b(\d{2})/(\d{2})/(\d{4})\b`),
+					{Pattern: regexp.MustCompile(`(?s).*`)},
+					{Pattern: regexp.MustCompile(`(?s)\b(\d{2})/(\d{2})/(\d{4})\b`),
 						Template: &[]string{"${3}-${1}-${2}"}[0]},
 				},
 			},
@@ -220,8 +221,8 @@ func TestBlockOptions(t *testing.T) {
 			want: blockOptions{
 				AllowYAMLLists: true,
 				ByRegex: []ByRegexOption{
-					{Pattern: regexp.MustCompile(`foo, bar`)},
-					{Pattern: regexp.MustCompile(`\b(\d{2})/(\d{2})/(\d{4})\b`),
+					{Pattern: regexp.MustCompile(`(?s)foo, bar`)},
+					{Pattern: regexp.MustCompile(`(?s)\b(\d{2})/(\d{2})/(\d{4})\b`),
 						Template: &[]string{"${3}-${1}-${2}"}[0]},
 				},
 			},