Edward Jones has agreed to pay more than $20 million to settle SEC charges that it overpriced new issues of municipal bonds.

The SEC alleged that from February 2009 to December 2012, the firm took new bonds into inventory and marked them up to customers during the offering period, or sold new-issue bonds at higher prices once secondary trading began.

Edward Jones generated at least $4.6 million in additional revenue through the scheme, which involved about 156 different bonds in which the firm served as a co-manager, the SEC said in its settlement document.

That ill-gotten gain was in addition to fees that Edward Jones earned as a member of underwriting syndicates, the SEC said.

The firm will set up a disgorgement fund of $5.2 million to pay back customers, and pay a fine to the SEC and MSRB of $15 million.

Also charged in the case was the Edward Jones’ former head of municipal underwriting, Stina Wishman.

Wishman settled for $15,000 and a two-year bar. She retired from Edward Jones in July 2014.

Edward Jones and Wishman did not admit or deny the charges.

Additionally, the firm was charged with general supervisory failures in its review of secondary-market municipal bond trades.

“Because current rules do not require dealers to disclose markups on municipal bonds, investors receive very little information about their dealer’s compensation in municipal bond trades,” said LeeAnn Ghazil Gaunt, chief of the SEC enforcement division’s municipal unit, in a statement.

Beginning in 2013, Edward Jones undertook some remedial measures to boost compliance efforts, including the disclosure of markups and markdowns, the SEC said.

In one instance, the firm’s mispricing resulted in an adverse federal tax determination for some Build America Bonds issued by the Nebraska Public Power District (NPPD) in 2009. In July 2013, the NPPD resolved the tax dispute by paying $350,000 to the IRS. Edward Jones later agreed to reimburse the NPPD for the tax penalty.

The settlement involves about 13,000 current and former Edward Jones clients, said Edward Jones spokesman John Boul.

“Those folks will all be fully compensated with interest,” Boul said.

The firm has “cooperated fully” with the SEC on the investigation which began about three years ago, he added, “and the SEC acknowledged in its order the positive steps we’ve taken” to improve supervision.