The need for novel antibiotics to combat emerging multi-drug resistant bacterial strains is widely acknowledged. The development of new therapeutic agents relies on small and medium-sized biotechnology enterprises (SMEs), representing 75% of the late-stage pipeline. However, most SME sponsors of an antibacterial approved by the FDA since 2010 have gone bankrupt, or exited at a loss, below investment cost. Uncovering financial flows related to the development and commercialisation of a single drug is complex and typically untransparent. There is therefore a lack of empirical research on the financial vulnerabilities of these critical SMEs. The development of plazomicin by Achaogen (2004–2019) entailed financial disclosures as a public company enabling application of financial analysis methods to: determine quantum and timing of public and private investments; quantify development costs; and provide a deeper understanding of the role of capital market dependency in exacerbating pipeline fragility. Achaogen’s widely cited bankruptcy, and plazomicin’s commercialisation failure, created a perception that novel antibiotics have zero market value, causing investors to question the SME developer business model. Our analysis of Achaogen’s inability to fund commercialisation suggests three key implications for the antibiotic investment ecosystem: (1) novel antibiotics with narrow approval for small patient populations affected by severe resistant infections cannot be successfully commercialised in the current US antibiotic market; (2) SMEs need incentive payments structured to enable them to survive the commercialisation cashflow drought, and (3) these changes are necessary to restore industry and financial investor confidence in the antibiotic SME development model. Achaogen’s demise demonstrates that proposals to incentivise innovation, e.g. by providing one-off payments at registration, may be insufficient to ensure access to novel antibiotics developed by SMEs. In plazomicin’s case, moreover, US government biosecurity investments have not resulted in access, as the Indian and Chinese companies which bought post-bankruptcy rights have not widely commercialised the drug. This study is timely as new market-based incentives are currently being proposed by the US, EU, Canada and Japan. In order to make further government funding effective, ensuring access, not only innovation, these must support sustainable financial models for the SMEs critical to novel antibiotic development.