diff --git a/src/puya/compile.py b/src/puya/compile.py
index 6274524de3..21ac20de1d 100644
--- a/src/puya/compile.py
+++ b/src/puya/compile.py
@@ -33,6 +33,7 @@
     ContractReference,
     DebugInfo,
     LogicSignatureMetaData,
+    LogicSigProgramReference,
     LogicSigReference,
     TemplateValue,
 )
@@ -194,7 +195,7 @@ def _dummy_program() -> _CompiledProgram:
 
     return _CompiledProgram(
         teal=TealProgram(
-            id="",
+            ref=LogicSigProgramReference(LogicSigReference()),
             avm_version=0,
             main=TealSubroutine(
                 is_main=True,
@@ -256,16 +257,20 @@ def _logic_sig_to_teal(
 
 
 def _compile_program(context: CompileContext, program: TealProgram) -> _CompiledProgram:
+    # if bytecode isn't required for this program, then only produce debug info
+    debug_only = (
+        not context.options.output_bytecode or program.ref.reference not in context.compilation_set
+    )
     assembled = assemble_program(
         context,
         program,
         template_variables={k: (v, None) for k, v in context.options.template_variables.items()},
-        debug_only=not context.options.output_bytecode,
+        debug_only=debug_only,
     )
     return _CompiledProgram(
         teal=program,
         teal_src=emit_teal(context, program),
-        bytecode=assembled.bytecode if context.options.output_bytecode else None,
+        bytecode=assembled.bytecode if not debug_only else None,
         debug_info=assembled.debug_info,
         template_variables=assembled.template_variables,
     )
diff --git a/src/puya/ir/main.py b/src/puya/ir/main.py
index 56466162f6..9adef1258e 100644
--- a/src/puya/ir/main.py
+++ b/src/puya/ir/main.py
@@ -39,8 +39,11 @@
     ARC4Struct,
     ARC4StructField,
     ContractMetaData,
+    ContractProgramReference,
     ContractState,
     LogicSignatureMetaData,
+    LogicSigProgramReference,
+    ProgramReference,
     StateTotals,
 )
 from puya.parse import SourceLocation
@@ -274,7 +277,9 @@ def _build_ir(ctx: IRBuildContext, contract: awst_nodes.Contract) -> Contract:
             *(ctx.subroutines[ref] for ref in approval_subs_srefs),
             *ctx.embedded_funcs_lookup.values(),
         ),
-        program_id=".".join((contract.id, contract.approval_program.short_name)),
+        ref=ContractProgramReference(
+            reference=contract.id, program_name=contract.approval_program.short_name
+        ),
         avm_version=avm_version,
     )
     clear_state_ir = _make_program(
@@ -284,7 +289,9 @@ def _build_ir(ctx: IRBuildContext, contract: awst_nodes.Contract) -> Contract:
             *(ctx.subroutines[ref] for ref in clear_subs_srefs),
             *ctx.embedded_funcs_lookup.values(),
         ),
-        program_id=".".join((contract.id, contract.clear_program.short_name)),
+        ref=ContractProgramReference(
+            reference=contract.id, program_name=contract.clear_program.short_name
+        ),
         avm_version=avm_version,
     )
     result = Contract(
@@ -336,7 +343,7 @@ def _build_logic_sig_ir(
             *(ctx.subroutines[ref] for ref in program_sub_refs),
             *ctx.embedded_funcs_lookup.values(),
         ),
-        program_id=logic_sig.id,
+        ref=LogicSigProgramReference(reference=logic_sig.id),
         avm_version=coalesce(logic_sig.avm_version, ctx.options.target_avm_version),
     )
     result = LogicSignature(
@@ -421,7 +428,7 @@ def _make_program(
     main: awst_nodes.Function,
     references: Iterable[Subroutine],
     *,
-    program_id: str,
+    ref: ProgramReference,
     avm_version: int,
 ) -> Program:
     if main.args:
@@ -439,7 +446,7 @@ def _make_program(
     )
     FunctionIRBuilder.build_body(ctx, function=main, subroutine=main_sub)
     return Program(
-        id=program_id,
+        ref=ref,
         main=main_sub,
         subroutines=tuple(references),
         avm_version=avm_version,
diff --git a/src/puya/ir/models.py b/src/puya/ir/models.py
index d8032c78fc..dd9355c7b0 100644
--- a/src/puya/ir/models.py
+++ b/src/puya/ir/models.py
@@ -19,6 +19,7 @@
     ContractReference,
     LogicSignatureMetaData,
     LogicSigReference,
+    ProgramReference,
 )
 from puya.parse import SourceLocation
 from puya.utils import unique
@@ -935,7 +936,7 @@ class Program(Context):
     # return
     #
     # ie, just omit the subroutine header, and replace any&all retsub ops with a return instead
-    id: str
+    ref: ProgramReference
     main: Subroutine
     subroutines: Sequence[Subroutine]
     source_location: SourceLocation | None = None
diff --git a/src/puya/mir/main.py b/src/puya/mir/main.py
index b85c9d029c..a31de3b610 100644
--- a/src/puya/mir/main.py
+++ b/src/puya/mir/main.py
@@ -16,8 +16,8 @@ def program_ir_to_mir(
     ctx = attrs_extend(ProgramMIRContext, context, program=program_ir)
 
     result = models.Program(
-        id=program_ir.id,
-        main=_lower_subroutine_to_mir(ctx, program_ir.main, is_main=True, name=program_ir.id),
+        ref=program_ir.ref,
+        main=_lower_subroutine_to_mir(ctx, program_ir.main, is_main=True, name=program_ir.ref.id),
         subroutines=[
             _lower_subroutine_to_mir(ctx, ir_sub, is_main=False, name=ir_sub.full_name)
             for ir_sub in program_ir.subroutines
diff --git a/src/puya/mir/models.py b/src/puya/mir/models.py
index 5ec0536961..dd1293e15f 100644
--- a/src/puya/mir/models.py
+++ b/src/puya/mir/models.py
@@ -10,6 +10,7 @@
 from puya.avm_type import AVMType
 from puya.errors import InternalError
 from puya.ir.utils import format_bytes, format_error_comment
+from puya.models import ProgramReference
 
 if t.TYPE_CHECKING:
     from collections.abc import Iterable, Iterator, Mapping, Sequence
@@ -622,7 +623,7 @@ def get_block(self, block_name: str) -> MemoryBasicBlock:
 
 @attrs.define
 class Program:
-    id: str
+    ref: ProgramReference
     main: MemorySubroutine
     subroutines: list[MemorySubroutine]
     avm_version: int
diff --git a/src/puya/models.py b/src/puya/models.py
index 40faa8069c..6b05443520 100644
--- a/src/puya/models.py
+++ b/src/puya/models.py
@@ -21,6 +21,35 @@ class LogicSigReference(str):  # can't use typing.NewType with pattern matching
     __slots__ = ()
 
 
+class ProgramReference(abc.ABC):
+    @property
+    @abc.abstractmethod
+    def reference(self) -> ContractReference | LogicSigReference: ...
+
+    @property
+    @abc.abstractmethod
+    def id(self) -> str: ...
+
+
+@attrs.frozen
+class LogicSigProgramReference(ProgramReference):
+    reference: LogicSigReference
+
+    @property
+    def id(self) -> str:
+        return self.reference
+
+
+@attrs.frozen
+class ContractProgramReference(ProgramReference):
+    reference: ContractReference
+    program_name: str
+
+    @property
+    def id(self) -> str:
+        return f"{self.reference}.{self.program_name}"
+
+
 # values and names are matched to AVM definitions
 class OnCompletionAction(enum.IntEnum):
     NoOp = 0
diff --git a/src/puya/teal/main.py b/src/puya/teal/main.py
index 7f844a9f28..63b8979a7c 100644
--- a/src/puya/teal/main.py
+++ b/src/puya/teal/main.py
@@ -38,7 +38,7 @@ def _get_all_stack_manipulations(
 
 def _build_teal(mir_program: mir.Program) -> teal_models.TealProgram:
     program = teal_models.TealProgram(
-        id=mir_program.id,
+        ref=mir_program.ref,
         avm_version=mir_program.avm_version,
         main=TealBuilder.build_subroutine(mir_program.main),
         subroutines=[TealBuilder.build_subroutine(mir_sub) for mir_sub in mir_program.subroutines],
diff --git a/src/puya/teal/models.py b/src/puya/teal/models.py
index 52a5f47dbd..a0db53349a 100644
--- a/src/puya/teal/models.py
+++ b/src/puya/teal/models.py
@@ -7,7 +7,7 @@
 from puya.ir.types_ import AVMBytesEncoding
 from puya.ir.utils import format_bytes, format_error_comment
 from puya.mir.models import Signature
-from puya.models import OnCompletionAction, TransactionType
+from puya.models import OnCompletionAction, ProgramReference, TransactionType
 from puya.parse import SourceLocation
 from puya.utils import valid_bytes, valid_int64
 
@@ -518,7 +518,7 @@ class TealSubroutine:
 
 @attrs.define
 class TealProgram:
-    id: str
+    ref: ProgramReference
     avm_version: int
     main: TealSubroutine
     subroutines: list[TealSubroutine]
diff --git a/tests/test_assemble.py b/tests/test_assemble.py
index fc9dd8fd89..4b7a2f59d1 100644
--- a/tests/test_assemble.py
+++ b/tests/test_assemble.py
@@ -8,7 +8,13 @@
 
 from puya.context import CompileContext
 from puya.mir.models import Signature
-from puya.models import CompiledContract, CompiledLogicSig, CompiledProgram
+from puya.models import (
+    CompiledContract,
+    CompiledLogicSig,
+    CompiledProgram,
+    LogicSigProgramReference,
+    LogicSigReference,
+)
 from puya.options import PuyaOptions
 from puya.teal import models as teal
 from puya.ussemble.main import assemble_program
@@ -122,7 +128,7 @@ def test_assemble_last_op_jump() -> None:
             sources_by_path={},
         ),
         program=teal.TealProgram(
-            id="",
+            ref=LogicSigProgramReference(LogicSigReference()),
             avm_version=10,
             main=teal.TealSubroutine(
                 is_main=True,
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 64b2f2db17..4fbe03a658 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -87,6 +87,17 @@ def test_run_single_file() -> None:
     run_puyapy([TEST_CASES_DIR / Path("simple") / "contract.py"])
 
 
+def test_run_single_file_with_other_references(tmpdir: Path) -> None:
+    run_puyapy(
+        [
+            TEST_CASES_DIR / "compile" / "factory.py",
+            "--output-bytecode",
+            "--out-dir",
+            str(tmpdir),
+        ]
+    )
+
+
 def test_run_multiple_files() -> None:
     run_puyapy(
         [