X0202 SCHEDULE 13D/A 0001104659-18-066641 0001545458 XXXXXXXX LIVE 3 Class A Common Shares, par value US$0.000079365 10/05/2026 false 0001745431 G85158106 StoneCo Ltd.

4th Floor, Harbour Place 103 South Church Street, P.O. Box 10240 Grand Cayman E9 KY1-1002

Thomas Patterson (650) 854-8300 c/o Madrone Advisors, LLC P.O. Box #6476 Denver CO 80206 0001545458 N Madrone Partners, L.P. b WC N DE 0.00 24589276.00 0.00 24589276.00 24589276.00 N 10.6 PN 0001789147 N Madrone Capital Partners, LLC b AF N DE 0.00 24589276.00 0.00 24589276.00 24589276.00 N 10.6 OO 0001293780 N Jameson J. McJunkin b AF N X1 0.00 24911276.00 0.00 24911276.00 24911276.00 N 10.7 IN 0001214954 N Thomas Patterson b AF N X1 0.00 24589276.00 0.00 24589276.00 24589276.00 N 10.6 IN 0001353165 N Gregory Boyd Penner b WC PF N X1 0.00 25228161.00 0.00 25228161.00 25228161.00 N 10.8 IN Class A Common Shares, par value US$0.000079365 StoneCo Ltd. 4th Floor, Harbour Place 103 South Church Street, P.O. Box 10240 Grand Cayman E9 KY1-1002 This Amendment No. 3 (this "Amendment No. 3" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on November 7, 2018, and amended on December 12, 2018 and December 18, 2020 (as amended, the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 3 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. This Schedule 13D is being filed on behalf of Madrone Partners, L.P. ("Madrone"), Madrone Capital Partners, LLC ("Madrone GP"), Gregory Penner ("Penner"), Jameson McJunkin ("McJunkin") and Thomas Patterson ("Patterson"). The foregoing entities and individuals are collectively referred to herein as the "Reporting Persons." The agreement among the Reporting Persons to file this Schedule 13D jointly in accordance with Rule 13d-1(k) of the Act is filed as Exhibit 99.1. The business address of the Reporting Persons is P.O. Box #6476, Denver, CO 80206. The principal business of Madrone is venture capital investments. Madrone GP performs the functions of, and serves as, the sole general partner of Madrone. Each of Messrs. Penner, McJunkin and Patterson is a managing director of Madrone GP. During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors). During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws. Each of the entities was organized in the state of Delaware and each of the individuals is a United States citizen. Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D/A set forth the aggregate number of Class A common shares of the Issuer and percentage of the Class A common shares of the Issuer beneficially owned by such Reporting Person and are incorporated herein by reference. The percentage set forth in row 13 of each cover page is based upon 232,663,503 Class A common shares outstanding as of December 31, 2025, as reported in the Issuer's Annual Report on Form 20-F filed with the Securities and Exchange Commission (the "SEC") on April 23, 2026. The Reporting Persons' ownership of the Issuer's securities consists of (i) 24,589,276 Class A common shares directly held by Madrone; (ii) 322,000 Class A common shares held by McJunkin through the McJunkin Living Trust, of which he is a co-trustee; and (iii) 638,885 Class A common shares held by Penner through Shimoda Holdings LLC, a family LLC, of which he is a managing member. Madrone GP is the sole general partner of Madrone. McJunkin, Patterson and Penner are Managing Members of Madrone GP and may share voting and dispositive power over the shares held by Madrone. Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D/A set forth the number of Class A common shares of the Issuer as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated herein by reference. Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days. Weighted Low High Reporting Transaction No. of Average Price Price Transaction Person Date Shares Price ($) ($) ($) Open Market Sale Madrone 10/05/2026 750,000 11.90 11.75 12.02 The Reporting Persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the SEC, upon request, full information regarding the number of shares sold at each separate price within the ranges set forth above. No other person is known to have the right to receive or the power to direct the receipt of dividends from, or any proceeds from the sale of, the securities beneficially owned by any of the Reporting Persons. Not applicable. Exhibit 99.1 Joint Filing Agreement Madrone Partners, L.P. /s/ Thomas Patterson 10/07/2026 Madrone Capital Partners, LLC /s/ Thomas Patterson 10/07/2026 Jameson J. McJunkin /s/ Jameson McJunkin 10/07/2026 Thomas Patterson /s/ Thomas Patterson 10/07/2026 Gregory Boyd Penner /s/ Gregory Penner 10/07/2026