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SCHEDULE 13D/A 0001829126-25-008156 0001990517 XXXXXXXX LIVE 1 Common Stock, $0.01 par value 10/16/2025 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 b WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.1 PN R01 Fund LP's beneficial ownership of the reported securities is comprised of (i) 220,663 shares of the Issuer's Series D Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 35,306,080 shares of the Issuer's Common Stock, and (ii) 134,375 shares of the Issuer's Series E Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 21,500,000 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 6,010,749 shares of Common Stock outstanding as of October 1, 2025, as reported in the Issuer's Registration Statement on Form S-3, which was filed with the Securities and Exchange Commission on October 3, 2025, and 77,000,000 shares and 43,000,000 shares of Common Stock underlying the Series D Non-Voting Convertible Preferred Stock and Series E Non-Voting Convertible Preferred Stock, respectively. Y R01 Capital LLC b WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.1 OO R01 Fund LP's beneficial ownership of the reported securities is comprised of (i) 220,663 shares of the Issuer's Series D Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 35,306,080 shares of the Issuer's Common Stock, and (ii) 134,375 shares of the Issuer's Series E Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 21,500,000 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 6,010,749 shares of Common Stock outstanding as of October 1, 2025, as reported in the Issuer's Registration Statement on Form S-3, which was filed with the Securities and Exchange Commission on October 3, 2025, and 77,000,000 shares and 43,000,000 shares of Common Stock underlying the Series D Non-Voting Convertible Preferred Stock and Series E Non-Voting Convertible Preferred Stock, respectively. Y R01 Capital Manager LLC b WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.1 OO R01 Fund LP's beneficial ownership of the reported securities is comprised of (i) 220,663 shares of the Issuer's Series D Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 35,306,080 shares of the Issuer's Common Stock, and (ii) 134,375 shares of the Issuer's Series E Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 21,500,000 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 6,010,749 shares of Common Stock outstanding as of October 1, 2025, as reported in the Issuer's Registration Statement on Form S-3, which was filed with the Securities and Exchange Commission on October 3, 2025, and 77,000,000 shares and 43,000,000 shares of Common Stock underlying the Series D Non-Voting Convertible Preferred Stock and Series E Non-Voting Convertible Preferred Stock, respectively. Y Michael Kazley b WC N DE 0.00 56806080.00 0.00 56806080.00 56806080.00 N 45.1 IN R01 Fund LP's beneficial ownership of the reported securities is comprised of (i) 220,663 shares of the Issuer's Series D Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 35,306,080 shares of the Issuer's Common Stock, and (ii) 134,375 shares of the Issuer's Series E Non-Voting Convertible Preferred Stock, which is convertible into a maximum of 21,500,000 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 6,010,749 shares of Common Stock outstanding as of October 1, 2025, as reported in the Issuer's Registration Statement on Form S-3, which was filed with the Securities and Exchange Commission on October 3, 2025, and 77,000,000 shares and 43,000,000 shares of Common Stock underlying the Series D Non-Voting Convertible Preferred Stock and Series E Non-Voting Convertible Preferred Stock, respectively. Common Stock, $0.01 par value NovaBay Pharmaceuticals, Inc. Explanatory Note: This Amendment No. 1 amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on October 15, 2025 (as amended, the "Statement") by the Reporting Persons with respect to the Common Stock of NovaBay Pharmaceuticals, Inc. (the "Company"). Unless otherwise defined herein, capitalized terms used in this Amendment No. 1 shall have the meanings ascribed to them in the Statement. Unless amended or otherwise stated below, the information in the Statement remains unchanged. This Amendment No. 1 is being filed to report (i) the convertibility of the Series D Non-Voting Convertible Preferred Stock following approval by the Stockholders at the Meeting and (ii) the issuance to the Reporting Persons of 134,375 shares of the Issuer's Series E Preferred Stock that are convertible, at the holder's election, into 21,500,000 shares of Common Stock. The Reporting Persons each beneficially own an aggregate of 56,806,080 shares of Common Stock (the "Subject Shares"). The Subject Shares represent approximately 45.1% of the outstanding shares of Common Stock, based on the aggregate of 6,010,749 shares of Common Stock outstanding as of October 1, 2025, as reported in the Issuer's Registration Statement on Form S-3, which was filed with the Securities and Exchange Commission on October 3, 2025, and 77,000,000 shares and 43,000,000 shares of Common Stock underlying the Series D Non-Voting Convertible Preferred Stock and Series E Non-Voting Convertible Preferred Stock, respectively, each of which were approved at the Meeting. 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. On October 15, 2025, the Reporting Persons entered into a pre-funded warrant contract with the Company pursuant to which they purchased the right to purchase a total of 2,702,703 shares of Common Stock. The warrant is not exercisable at all until January 1, 2026 and not exercisable in its entirety until the Stockholders approve the issuance of the 2,702,703 shares of Common Stock subject to the warrant. Exhibit 99.1: Form of Pre-Funded Warrant (incorporated by reference to the Company's current report on Form 8-K filed on October 20, 2025). https://www.sec.gov/Archives/edgar/data/1389545/000182912625008237/novabay_ex4-1.htm R01 Fund LP /s/ Michael Kazley Michael Kazley / Principal 10/20/2025 R01 Capital LLC /s/ Michael Kazley Michael Kazley / Managing Member 10/20/2025 R01 Capital Manager LLC /s/ Michael Kazley Michael Kazley / Managing Member 10/20/2025 Michael Kazley /s/ Michael Kazley Michael Kazley 10/20/2025