What is the best approach for serializing BigDecimal/BigInteger to ProtocolBuffers

Yes. You should define BigInteger as BigInteger.toByteArray() .

My guess is that BigDecimal would be:

message BDecimal {
  required int32 scale = 1;
  required BInteger int_val = 2;
}

while BigInteger may be defined as

message BInteger {
  required bytes value = 1;
}

The code to handle BigInteger would be:

  BInteger write(BigInteger val) {
    BInteger.Builder builder = BInteger.newBuilder();
    ByteString bytes = ByteString.copyFrom(val.toByteArray());
    builder.setValue(bytes);
    return builder.build();
  }

  BigInteger read(BInteger message) {
    ByteString bytes = message.getValue();
    return new BigInteger(bytes.toByteArray());
  }