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SCHEDULE 13D/A 0001829126-25-008156 0001990517 XXXXXXXX LIVE 2 Common Stock, $0.01 par value 01/16/2026 false 0001389545 66987P409 NovaBay Pharmaceuticals, Inc. 2000 POWELL STREET, SUITE 1150 EMERYVILLE CA 94608 R01 FUND LP 305-982-7994 1111 Lincoln Road Suite 500 Miami Beach FL 33139 0001990517 N R01 Fund LP a WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.0 PN R01 Fund LP's beneficial ownership of the reported securities is comprised of 56,806,080 shares of the Issuer's Common Stock. The reported securities may also be deemed beneficially owned by R01 Capital LLC, R01 Capital Manager LLC and Michael Kazley, each of which or whom disclaim beneficial ownership of these shares, except to the extent of its or his pecuniary interest in such shares, if any. All percentage calculations herein are based on the aggregate of 126,173,650 shares of Common Stock outstanding as of January 16, 2026. 0002091715 N R01 Capital LLC a WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.0 OO R01 Fund LP's beneficial ownership of the reported securities is comprised of 56,806,080 shares of the Issuer's Common Stock. The reported securities may also be deemed beneficially owned by R01 Capital LLC, R01 Capital Manager LLC and Michael Kazley, each of which or whom disclaim beneficial ownership of these shares, except to the extent of its or his pecuniary interest in such shares, if any. All percentage calculations herein are based on the aggregate of 126,173,650 shares of Common Stock outstanding as of January 16, 2026. 0002091724 N R01 Capital Manager LLC a WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.0 OO R01 Fund LP's beneficial ownership of the reported securities is comprised of 56,806,080 shares of the Issuer's Common Stock. The reported securities may also be deemed beneficially owned by R01 Capital LLC, R01 Capital Manager LLC and Michael Kazley, each of which or whom disclaim beneficial ownership of these shares, except to the extent of its or his pecuniary interest in such shares, if any. All percentage calculations herein are based on the aggregate of 126,173,650 shares of Common Stock outstanding as of January 16, 2026. 0002091727 N Kazley Michael John a WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.0 IN R01 Fund LP's beneficial ownership of the reported securities is comprised of 56,806,080 shares of the Issuer's Common Stock. The reported securities may also be deemed beneficially owned by R01 Capital LLC, R01 Capital Manager LLC and Michael Kazley, each of which or whom disclaim beneficial ownership of these shares, except to the extent of its or his pecuniary interest in such shares, if any. All percentage calculations herein are based on the aggregate of 126,173,650 shares of Common Stock outstanding as of January 16, 2026. Common Stock, $0.01 par value NovaBay Pharmaceuticals, Inc. 2000 POWELL STREET, SUITE 1150 EMERYVILLE CA 94608 Explanatory Note: This Amendment No. 2 amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on October 15, 2025, as amended and supplemented by that certain Amendment No. 1 to Schedule 13D filed on October 25, 2025 (as amended, the "Statement") by R01 Fund LP ("R01") with respect to the Common Stock of NovaBay Pharmaceuticals, Inc. (the "Company"). Unless otherwise defined herein, capitalized terms used in this Amendment No. 2 shall have the meanings ascribed to them in the Statement. Unless amended or otherwise stated below, the information for R01 in the Statement remains unchanged. This Amendment No. 2 is being filed to report the Reporting Persons identifying as a "group" with Framework Ventures IV L.P., Framework Ventures Management LLC, Framework Ventures IV GP LLC, Vance Spencer and Michael Ernest Anderson for purposes of Rule 13d-3 under the Exchange Act. The Reporting Persons have agreed to file this Amendment jointly as a group pursuant to Rule 13d-1(k) under the Exchange Act. On January 16, 2026, the Company, R01 and Framework Ventures IV L.P. ("Framework") entered into a securities purchase agreement (the "Securities Purchase Agreement"), pursuant to which R01 and Framework purchased pre-funded warrants exercisable for shares of Common Stock (the "January 2026 Pre-Funded Warrants") for a purchase price of $0.17 per share of underlying Common Stock. The January 2026 Pre-Funded Warrants are not exercisable until six months after issuance; accordingly, the shares underlying such warrants are not deemed beneficially owned by the Reporting Persons for purposes of this Statement under Rule 13d-3 and are excluded from the ownership percentages reported herein. The 2026 Pre-Funded Warrants vest on a tiered basis, with 20% of the 2026 Pre-Funded Warrants becoming exercisable 6 months after execution of the Securities Purchase Agreement, 30% of the 2026 Pre-Funded Warrants becoming exercisable 9 months after execution of the Securities Purchase Agreement and the remaining 50% of the 2026 Pre-Funded Warrants becoming exercisable 12 months after execution of the Securities Purchase Agreement, each subject to receipt of stockholder approval. In connection with the same transaction, the Company and certain purchasers, including R01, entered into an investors' rights agreement (the "Investors' Rights Agreement") that, among other things, provides R01: (1) customary demand rights for their shares of Common Stock underlying the January 2026 Pre-Funded Warrants, (2) customary piggyback registration rights and (3) nomination rights to appoint one director to the Board. The Reporting Persons beneficially own an aggregate of 56,806,080 shares of Common Stock (the "Subject Shares"). The Subject Shares represent approximately 45.0% of the outstanding shares of Common Stock, based on the aggregate of 126,173,650 shares of Common Stock outstanding as of January 16, 2026. 1. Sole power to vote or direct vote: 0.00 2. Shared power to vote or direct vote: 56,806,080 shares of Common Stock 3. Sole power to dispose or direct the disposition: 0.00 4. Shared power to dispose or direct the disposition: 56,806,080 shares of Common Stock Except as described in this Schedule 13D, none of the Reporting Persons have effected any transaction in the shares of Common Stock during the past 60 days. No person other than the Reporting Persons is known to have the right to receive, or the power to direct the receipt of dividends from, or proceeds from the sale of, the Subject Shares. Not applicable. As described in Item 4 above, on January 16, 2026, the Company, R01 and Framework entered into the Securities Purchase Agreement and the Investors' Rights Agreement. The descriptions of the Securities Purchase Agreement and the Investors' Rights Agreement above do not purport to be complete and are qualified in their entirety by reference to the Securities Purchase Agreement and the Investors' Rights Agreement, which are filed as exhibits to this Amendment No. 2 to Schedule 13D, and are incorporated by reference herein. Exhibit 99.1: Form of Pre-Funded Warrant (incorporated by reference to the Company's current report on Form 8-K filed on January 16, 2026). Exhibit 99.2: Investors' Rights Agreement (incorporated by reference to the Company's current report on Form 8-K filed on January 16, 2026). R01 Fund LP /s/ Michael Kazley Michael Kazley / Principal 01/21/2026 R01 Capital LLC /s/ Michael Kazley Michael Kazley / Managing Member 01/21/2026 R01 Capital Manager LLC /s/ Michael Kazley Michael Kazley / Managing Member 01/21/2026 Kazley Michael John /s/ Michael Kazley Michael Kazley 01/21/2026