Parent company Oaxaca Ltd posted a pre-tax loss of £4.9m for the 12 months to 24 June 2018, down from a £4.7m loss the previous year.
Turnover rose slightly from £46.6m to £47.9m.
Wahaca was forced to close nine of its 25 restaurants in October 2017 after over 100 diners reportedly fell ill.
The group last posted a profit, of £600,000, in the year to 26 June 2016.
Co-founder Mark Selby wrote in the most recent filings that Wahaca had “demonstrated stable growth…as it continued to recover from a one off event in October 2016. This was achieved against a backdrop of challenging market conditions and continued in to the current financial year”.
He adds that though the restaurant market remained “competitive”, Wahaca's investment in its teams and sustainability of products meant it had a competitive advantage “in the long run”.
Selby co-founded Wahaca with MasterChef winner Thomasina Miers in 2007.