Strong regional variation, together with the lack of standard orthography, makes Swiss German automatic speech recognition (ASR) particularly difficult in a multi-dialectal setting. This paper focuses on one of the many challenges, namely, the choice of the output text to represent non-standardised Swiss German. We investigate two potential options: a) dialectal writing – approximate phonemic transcriptions that provide close correspondence between grapheme labels and the acoustic signal but are highly inconsistent and b) normalised writing – transcriptions resembling standard German that are relatively consistent but distant from the acoustic signal. To find out which writing facilitates Swiss German ASR, we build several systems using the Kaldi toolkit and a dataset covering 14 regional varieties. A formal comparison shows that the system trained on the normalised transcriptions achieves better results in word error rate (WER) (29.39%) but underperforms at the character level, suggesting dialectal transcriptions offer a viable solution for downstream applications where dialectal differences are important. To better assess word-level performance for dialectal transcriptions, we use a flexible WER measure (FlexWER). When evaluated with this metric, the system trained on dialectal transcriptions outperforms that trained on the normalised writing. Besides establishing a benchmark for Swiss German multi-dialectal ASR, our findings can be helpful in designing ASR systems for other languages without standard orthography.