diff --git a/regex/operators/assembler.go b/regex/operators/assembler.go
index 8a906c8..2540d64 100644
--- a/regex/operators/assembler.go
+++ b/regex/operators/assembler.go
@@ -129,12 +129,11 @@ func (a *Operator) complete(assembleParser *parser.Parser) (string, error) {
 		return "", err
 	}
 
-	if len(assembleParser.Prefixes) > 0 && len(assembleParser.Suffixes) > 0 && len(result) > 0 {
-		result = "(?:" + result + ")"
-	}
-	prefixes := strings.Join(assembleParser.Prefixes, "")
-	suffixes := strings.Join(assembleParser.Suffixes, "")
-	result = prefixes + result + suffixes
+	// Note: Prefix/suffix application is now handled by individual Assemble processors (block-scoped).
+	// Prefix/suffix directives are passed through as raw lines, so they are not applied here.
+	// Parser.Prefixes and Parser.Suffixes record which directives a file contained; the parser
+	// uses that to decide whether an included file needs its own assemble block, and the operator
+	// path does not read them.
 
 	if len(result) > 0 {
 		logger.Trace().Msgf("Applying last cleanups to %s\n", result)
diff --git a/regex/operators/assembler_test.go b/regex/operators/assembler_test.go
index 396a435..b376687 100644
--- a/regex/operators/assembler_test.go
+++ b/regex/operators/assembler_test.go
@@ -4,7 +4,9 @@
 package operators
 
 import (
+	"io/fs"
 	"os"
+	"path"
 	"testing"
 
 	"github.com/stretchr/testify/suite"
@@ -832,6 +834,7 @@ d
 
 }
 func (s *assemblerTestSuite) TestAssemble_ConcatenationWithPrefixAndSuffix() {
+	// Test that top-level prefix/suffix apply to the implicit top-level block
 	contents := `##!^ prefix
 ##!$ suffix
   ##!> assemble
@@ -1121,3 +1124,217 @@ func (s *assemblerTestSuite) TestAssemble_ValidateCharacterClass() {
 
 	s.ErrorContains(err, "unicode hex escape codepoint too big: 1114111 > 255")
 }
+
+// Test block-scoped prefix/suffix behavior
+func (s *assemblerTestSuite) TestAssemble_BlockScopedPrefixSuffix_InsideBlock() {
+	// Test that prefix/suffix inside an assemble block are block-scoped
+	contents := `##!> assemble
+##!^ prefix
+##!$ suffix
+a
+b
+##!<`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// wrapCompletedAssembly already wraps in (?:...)
+	s.Equal(`prefix[ab]suffix`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_BlockScopedPrefixSuffix_TopLevel() {
+	// Verify top-level directives still work (implicit top-level block)
+	contents := `##!^ prefix
+##!$ suffix
+a
+b`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	s.Equal(`prefix[ab]suffix`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_BlockScopedPrefixSuffix_MultipleBlocks() {
+	// Test multiple assemble blocks with different prefix/suffix in each
+	contents := `##!> assemble
+##!^ prefix1
+a
+b
+##!<
+##!=>
+##!> assemble
+##!$ suffix2
+c
+d
+##!<`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// Each block applies its own prefix/suffix independently
+	s.Equal(`prefix1[ab][cd]suffix2`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_BlockScopedPrefixSuffix_NestedPattern() {
+	// Test the pattern from 934160.ra - prefix/suffix at start of assemble block
+	contents := `##!> assemble
+##!^ while\s*\([\s(]*
+##!$ .*\)
+true
+false
+##!<`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// Note: assembler applies various transformations like \s -> [\s\x0b]
+	// We just check that prefix/suffix are applied
+	s.Contains(output, `while`)
+	s.Contains(output, `.*\)`)
+	s.Contains(output, `tru`)
+	s.Contains(output, `fals`)
+}
+
+// writeIncludeFile writes an include file that `##!> include name` will resolve.
+func (s *assemblerTestSuite) writeIncludeFile(name string, contents string) {
+	s.T().Helper()
+	includeDir := path.Join(s.tempDir, "regex-assembly", "include")
+	s.Require().NoError(os.MkdirAll(includeDir, fs.ModePerm))
+	s.Require().NoError(os.WriteFile(path.Join(includeDir, name+".ra"), []byte(contents), fs.ModePerm))
+}
+
+func (s *assemblerTestSuite) TestAssemble_IncludedPrefixIsScopedToIncludedContent() {
+	s.writeIncludeFile("scoped_prefix", "##!^ PRE_\nalpha\n")
+
+	// `beta` belongs to the including file and must not pick up the include's prefix,
+	// no matter which side of the include it sits on.
+	for _, tt := range []struct {
+		name     string
+		contents string
+		expected string
+	}{
+		{"caller line after include", "##!> include scoped_prefix\nbeta", `(?:PRE_alph|bet)a`},
+		{"caller line before include", "beta\n##!> include scoped_prefix", `(?:bet|PRE_alph)a`},
+		{"caller lines on both sides", "gamma\n##!> include scoped_prefix\nbeta", `(?:gamm|PRE_alph|bet)a`},
+	} {
+		s.Run(tt.name, func() {
+			output, err := NewAssembler(s.ctx).Run(tt.contents)
+			s.Require().NoError(err)
+			s.Equal(tt.expected, output)
+		})
+	}
+}
+
+func (s *assemblerTestSuite) TestAssemble_IncludedSuffixIsScopedToIncludedContent() {
+	s.writeIncludeFile("scoped_suffix", "##!$ _SUF\nalpha\n")
+
+	output, err := NewAssembler(s.ctx).Run("##!> include scoped_suffix\nbeta")
+	s.Require().NoError(err)
+	s.Equal(`alpha_SUF|beta`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_PrefixSuffixWithStashing() {
+	// Test that prefixes/suffixes are applied when storing expressions with ##!=<
+	contents := `##!> assemble
+##!^ prefix
+##!$ suffix
+a
+b
+##!=< stored
+##!<
+##!=> stored`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// The stored expression should include the prefix/suffix from its block
+	s.Equal(`prefix[ab]suffix`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_PrefixSuffixWithStashing_MultipleBlocks() {
+	// Test that each block's prefix/suffix are independently applied when stashing
+	contents := `##!> assemble
+##!^ prefix1
+##!$ suffix1
+a
+b
+##!=< block1
+##!<
+##!> assemble
+##!^ prefix2
+##!$ suffix2
+c
+d
+##!=< block2
+##!<
+##!=> block1
+##!=> block2`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// Each stored expression should have its own block's prefix/suffix
+	s.Equal(`prefix1[ab]suffix1prefix2[cd]suffix2`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_PrefixSuffixWithStashing_NoPrefix() {
+	// Test stashing without prefix/suffix works as before
+	contents := `##!> assemble
+a
+b
+##!=< stored
+##!<
+##!=> stored`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// No prefix/suffix should be applied
+	s.Equal(`[ab]`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_PrefixSuffixWithStashing_OnlyPrefix() {
+	// Test stashing with only prefix
+	contents := `##!> assemble
+##!^ prefix
+a
+b
+##!=< stored
+##!<
+##!=> stored`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// Only prefix should be applied
+	s.Equal(`prefix[ab]`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_BlockScopedPrefixSuffix_MultipleNestingLevels() {
+	// Test that prefix/suffix is correctly scoped when blocks are nested multiple levels deep.
+	// The outer block's prefix/suffix wraps the inner block's output, while the inner block's
+	// prefix/suffix only applies to the inner block's content.
+	contents := `##!> assemble
+##!^ outer_prefix
+##!$ outer_suffix
+##!> assemble
+##!^ inner_prefix
+##!$ inner_suffix
+a
+b
+##!<
+##!<`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	s.Equal(`outer_prefixinner_prefix[ab]inner_suffixouter_suffix`, output)
+}
+
+func (s *assemblerTestSuite) TestAssemble_PrefixSuffixWithStashing_OnlySuffix() {
+	// Test stashing with only suffix
+	contents := `##!> assemble
+##!$ suffix
+a
+b
+##!=< stored
+##!<
+##!=> stored`
+	assembler := NewAssembler(s.ctx)
+	output, err := assembler.Run(contents)
+	s.Require().NoError(err)
+	// Only suffix should be applied
+	s.Equal(`[ab]suffix`, output)
+}
diff --git a/regex/parser/include_test.go b/regex/parser/include_test.go
index f6c39ec..0b46024 100644
--- a/regex/parser/include_test.go
+++ b/regex/parser/include_test.go
@@ -72,11 +72,11 @@ func (s *parserIncludeTestSuite) TestParserInclude_Prefixes() {
 included regex`, "data regex")
 	parser := NewParser(s.ctx, s.reader)
 	actual := parser.Parse(false)
+	// Directives are passed through as-is, wrapped in an assemble block that scopes
+	// them to the included content instead of the rest of the including file.
 	expected := bytes.NewBufferString(`##!> assemble
-prefix1
-##!=>
-prefix2
-##!=>
+##!^ prefix1
+##!^ prefix2
 included regex
 ##!<
 data regex
@@ -90,13 +90,12 @@ func (s *parserIncludeTestSuite) TestParserInclude_Suffixes() {
 included regex`, "data regex")
 	parser := NewParser(s.ctx, s.reader)
 	actual := parser.Parse(false)
+	// Directives are passed through as-is, wrapped in an assemble block that scopes
+	// them to the included content instead of the rest of the including file.
 	expected := bytes.NewBufferString(`##!> assemble
+##!$ suffix1
+##!$ suffix2
 included regex
-##!=>
-suffix1
-##!=>
-suffix2
-##!=>
 ##!<
 data regex
 `)
@@ -112,17 +111,14 @@ func (s *parserIncludeTestSuite) TestParserInclude_FlagsPrefixesSuffixes() {
 included regex`, "data regex")
 	parser := NewParser(s.ctx, s.reader)
 	actual := parser.Parse(false)
+	// Directives are passed through as-is, wrapped in an assemble block that scopes
+	// them to the included content instead of the rest of the including file.
 	expected := bytes.NewBufferString(`##!> assemble
-prefix1
-##!=>
-prefix2
-##!=>
+##!$ suffix1
+##!$ suffix2
+##!^ prefix1
+##!^ prefix2
 included regex
-##!=>
-suffix1
-##!=>
-suffix2
-##!=>
 ##!<
 data regex
 `)
diff --git a/regex/parser/parser.go b/regex/parser/parser.go
index b6816a3..fb5fcbd 100644
--- a/regex/parser/parser.go
+++ b/regex/parser/parser.go
@@ -150,9 +150,15 @@ func (p *Parser) Parse(formatOnly bool) *bytes.Buffer {
 				}
 			}
 		case prefix:
+			// Pass the directive through for the Assemble processor to apply (block-scoped).
+			// Prefixes is still recorded so that parseFile knows whether an included file
+			// needs its own assemble block to scope these directives to its content.
 			p.Prefixes = append(p.Prefixes, parsedLine.prefix)
+			text = line + "\n"
 		case suffix:
+			// See the prefix case above.
 			p.Suffixes = append(p.Suffixes, parsedLine.suffix)
+			text = line + "\n"
 		}
 		if formatOnly {
 			text = line + "\n"
@@ -275,7 +281,7 @@ func parseFile(rootParser *Parser, filename string, definitions map[string]strin
 		newP.variables = definitions
 	}
 	out := newP.Parse(false)
-	newOut, err := mergePrefixesSuffixes(newP, out)
+	newOut, err := scopeIncludedFileDirectives(newP, out)
 	if err != nil {
 		logger.Fatal().Msgf("error parsing file: %v", err.Error())
 	}
@@ -283,16 +289,18 @@ func parseFile(rootParser *Parser, filename string, definitions map[string]strin
 	return newOut, newP.variables
 }
 
-// Merge prefixes, and suffixes from include files into another parser.
-// All of these need to be treated as local to the source parser.
+// Scope prefixes and suffixes from an included file to the content of that file.
+// The directives themselves are passed through as raw lines for the Assemble processor
+// to apply, so they need an assemble block of their own. Without it they stay active
+// for the rest of the including file and wrap the caller's content as well.
 // We removed flag merging because of https://github.com/coreruleset/crs-toolchain/issues/72
-func mergePrefixesSuffixes(source *Parser, out *bytes.Buffer) (*bytes.Buffer, error) {
-	logger.Trace().Msg("merging prefixes, suffixes from included file")
+func scopeIncludedFileDirectives(source *Parser, out *bytes.Buffer) (*bytes.Buffer, error) {
+	logger.Trace().Msg("scoping prefixes, suffixes from included file")
 	// If the included file has flags, this is an error
 	if len(source.Flags) > 0 {
 		return new(bytes.Buffer), errors.New("include files must not contain flags. See https://github.com/coreruleset/crs-toolchain/v2/issues/71")
 	}
-	// IMPORTANT: don't write the assemble block at all if there are no flags, prefixes, or
+	// IMPORTANT: don't write the assemble block at all if there are no prefixes or
 	// suffixes. Enclosing the output in an assemble block can change the semantics, for example,
 	// when the included content is processed by the cmdline processor in the including file.
 	if len(source.Prefixes) == 0 && len(source.Suffixes) == 0 {
@@ -301,32 +309,12 @@ func mergePrefixesSuffixes(source *Parser, out *bytes.Buffer) (*bytes.Buffer, er
 
 	newOut := new(bytes.Buffer)
 	newOut.WriteString("##!> assemble\n")
-
-	for _, prefix := range source.Prefixes {
-		newOut.WriteString(prefix)
-		newOut.WriteString("\n##!=>\n")
-	}
 	if _, err := out.WriteTo(newOut); err != nil {
 		logger.Fatal().Err(err).Msg("failed to copy output to new buffer")
 	}
-
-	sawNewLine := false
-	if err := out.UnreadByte(); err == nil {
-		lastByte, err := out.ReadByte()
-		if err == nil {
-			sawNewLine = lastByte == 13
-		}
-	}
-	if sawNewLine {
+	if !bytes.HasSuffix(newOut.Bytes(), []byte("\n")) {
 		newOut.WriteString("\n")
 	}
-	if len(source.Suffixes) > 0 {
-		newOut.WriteString("##!=>\n")
-	}
-	for _, suffix := range source.Suffixes {
-		newOut.WriteString(suffix)
-		newOut.WriteString("\n##!=>\n")
-	}
 	newOut.WriteString("##!<\n")
 	return newOut, nil
 }
diff --git a/regex/processors/assemble.go b/regex/processors/assemble.go
index c3272c4..6c2c93e 100644
--- a/regex/processors/assemble.go
+++ b/regex/processors/assemble.go
@@ -19,8 +19,10 @@ const (
 )
 
 type Assemble struct {
-	proc   *Processor
-	output strings.Builder
+	proc     *Processor
+	output   strings.Builder
+	prefixes []string
+	suffixes []string
 }
 
 // NewAssemble creates a new assemble processor
@@ -32,7 +34,23 @@ func NewAssemble(ctx *Context) *Assemble {
 
 // ProcessLine applies the processors logic to a single line
 func (a *Assemble) ProcessLine(line string) error {
-	match := regex.AssembleInputRegex.FindStringSubmatch(line)
+	// Check for prefix directive
+	match := regex.PrefixRegex.FindStringSubmatch(line)
+	if len(match) > 0 {
+		a.prefixes = append(a.prefixes, match[1])
+		logger.Trace().Msgf("Added block-scoped prefix: %s", match[1])
+		return nil
+	}
+
+	// Check for suffix directive
+	match = regex.SuffixRegex.FindStringSubmatch(line)
+	if len(match) > 0 {
+		a.suffixes = append(a.suffixes, match[1])
+		logger.Trace().Msgf("Added block-scoped suffix: %s", match[1])
+		return nil
+	}
+
+	match = regex.AssembleInputRegex.FindStringSubmatch(line)
 	if len(match) > 0 {
 		if err := a.store(match[1]); err != nil {
 			logger.Error().Err(err).Msgf("Failed to store input: %s", line)
@@ -69,6 +87,13 @@ func (a *Assemble) Complete() ([]string, error) {
 	}
 
 	result := a.wrapCompletedAssembly(regex)
+
+	// Apply block-scoped prefixes and suffixes
+	if len(a.prefixes) > 0 || len(a.suffixes) > 0 {
+		result = strings.Join(a.prefixes, "") + result + strings.Join(a.suffixes, "")
+		logger.Trace().Msgf("Applied block-scoped prefixes/suffixes: %s", result)
+	}
+
 	logger.Trace().Msgf("Completed assembly: %s", result)
 
 	if result == "" {
@@ -102,6 +127,18 @@ func (a *Assemble) store(identifier string) error {
 	// the value we just stored
 	a.output.Reset()
 
+	// Apply block-scoped prefixes and suffixes to stored expressions
+	if len(a.prefixes) > 0 || len(a.suffixes) > 0 {
+		prefixes := strings.Join(a.prefixes, "")
+		suffixes := strings.Join(a.suffixes, "")
+		outputString = prefixes + outputString + suffixes
+		logger.Trace().Msgf("Applied block-scoped prefixes/suffixes to stored expression: %s", outputString)
+		// Clear prefixes/suffixes after applying to stored expression
+		// so they won't be applied again in Complete()
+		a.prefixes = nil
+		a.suffixes = nil
+	}
+
 	logger.Debug().Msgf("Storing expression at %s: %s", identifier, outputString)
 	a.proc.ctx.stash[identifier] = outputString
 	return nil