The pub chain said there have been 66 positive tests among its 41,564 employees in the 10 weeks since July 4. They were found in 50 of its 811 pubs.
The data comes as the UK enters a new round of restrictions to maintain the spread of the virus, with 3,330 daily new cases as of September 13.
From Monday, people cannot meet members of other households in groups of more than six, both outdoors and indoors, including in private homes.
Public venues respecting safety measures, such as places of worship, restaurants and hospitality venues, can still host larger numbers in total but groups of up to 6 must not mix or form larger groups.
Individual households or support bubbles of more than six can still gather together.
More government updates
Starting on Friday, it will be mandatory for hospitality businesses to have a system to collect NHS Test and Trace data and keep it for 21 days.
Later this month, the government will review plans to pilot larger audiences in venues to announce whether it can be permitted to return audiences to stadiums and conference centres from October 1.
Planned sports pilot events will be limited to smaller, safer numbers, with strict conditions to ensure social distancing, and will not take place in areas where incidence is high.
Finally, businesses in local lockdown areas have seen their opening hours restricted and it could be extended nation-wide in the future.
Shares in Wetherspoons shed 3% to 894.5p on Monday in the early afternoon.