A famed taqueria in San Francisco’s Mission District paid some $500,000 to settle claims it retaliated against workers for complaining about alleged wage underpayment and other employment law violations.

The Mexican restaurant, La Taqueria, had already paid the California Department of Industrial Relations $154,691 on allegations it failed to pay overtime over a three-year period. In addition, a $72,000 civil penalty was charged and paid for alleged failures to provide workers with accurate wage statements. San Francisco separately assessed the restaurant a $207,182 penalty on allegations it failed to comply with the city’s pay-or-play health-care expenditure ordinance and $85,000 for...