The Microsoft logo on a building in France. Michel Euler/Associated Press

Microsoft will pay a $14.4-million settlement after California’s Civil Rights Department accused the company of retaliation and discrimination against workers who take parental or disability leave or leave to care for a family member.

A multiyear investigation by the Civil Rights Department found that workers at Microsoft in California experience disadvantages in pay and promotion opportunities when they take these types of protected leave.

Employees who took protected leave would receive lower bonuses and unfavorable performance reviews, the department said in its complaint, filed in Santa Clara County. When Microsoft managers awarded annual bonuses, stock awards, or merit increases, they did not consider time on protected leave as a time when employees were actively working – although other forms of leave were not discounted, according to the complaint.

Women and people with disabilities were disproportionately affected, the department alleged.

Some Microsoft managers also allegedly commented negatively about employees who took leave, and workers have reported concerns with retaliation after requesting or taking protected leave.

“Microsoft’s challenged actions are ongoing and will continue to harm,” the complaint states.

Although Microsoft’s headquarters is in Redmond, Wash., it maintains offices and employees in California, mostly concentrated in the Bay Area.

Nearly all the money from the agreement will go toward current and former employees eligible for direct relief. A worker is eligible if they worked for Microsoft in California in 2017 or later for at least three months and took a leave of absence protected under state or federal law.

As part of the settlement, Microsoft agreed to hire an independent consultant to examine and recommend the company’s personnel policies to ensure managers do not consider time on protected leave in determining annual rewards and promotions.

The company also agreed to train managers and human resources personnel about this kind of discrimination and to ensure employees know how to raise complaints if they believe they were unfairly denied annual bonuses or other awards.

Additionally, the independent consultant will provide annual reports to the Civil Rights Department on how complaints of discrimination are received and processed.

Last month, California’s Civil Rights Department reached a $15-million settlement to resolve allegations of sexual harassment, discrimination and retaliation at Snap, the Santa Monica-based company that created the popular social media app Snapchat.