Bionano Genomics, Inc.

The consolidated financial statements of Bionano Genomics, Inc. (the Company) as of December 31, 2024 and 2023 and for each of the years then ended incorporated by reference in this prospectus and in the registration statement have been so incorporated in reliance on the report of BDO USA, P.C., an independent registered public accounting firm, given on the authority of said firm as experts in auditing and accounting. The report on the consolidated financial statements contains an explanatory paragraph regarding the Company’s ability to continue as a going concern.

Up to 2,032,520 Shares of Common Stock

Up to 2,032,520 Pre-Funded Warrants to Purchase up to 2,032,520 Shares of Common Stock

Up to 2,032,520 Series E Warrants to Purchase up to 2,032,520 Shares of Common Stock

Up to 2,032,520 Series F Warrants to Purchase up to 2,032,520 Shares of Common Stock

Up to 6,097,560 Shares of Common Stock Issuable Upon Exercise of the

Pre-Funded Warrants, Series E Warrants and Series F Warrants

PRELIMINARY PROSPECTUS

H.C. Wainwright & Co.

The date of this prospectus is , 2025.

PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

The following table sets forth the costs and expenses, other than placement agent fees and commissions, payable by us in connection with the sale and distribution of the securities being registered. All of the amounts shown are estimates, except for the SEC registration fee and the FINRA filing fee:

We are incorporated under the laws of the State of Delaware. Section 145 of the General Corporation Law of the State of Delaware provides that a Delaware corporation may indemnify any persons who were, are, or are threatened to be made, parties to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative (other than an action by or in the right of such corporation), by reason of the fact that such person is or was an officer, director, employee or agent of such corporation, or is or was serving at the request of such corporation as an officer, director, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys’ fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding, provided that such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation’s best interests and, with respect to any criminal action or proceeding, had no reasonable cause to believe that his or her conduct was illegal. A Delaware corporation may indemnify any persons who were, are, or are threatened to be made, a party to any threatened, pending or completed action or suit by or in the right of the corporation by reason of the fact that such person is or was a director, officer, employee or agent of such corporation, or is or was serving at the request of such corporation as a director, officer, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys’ fees) actually and reasonably incurred by such person in connection with the defense or settlement of such action or suit provided such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation’s best interests except that no indemnification is permitted without judicial approval if the officer or director is adjudged to be liable to the corporation. Where an officer or director is successful on the merits or otherwise in the defense of any action referred to above, the corporation must indemnify him or her against the expenses (including attorneys’ fees) actually and reasonably incurred.

Our amended and restated certificate of incorporation, as amended, and our amended and restated bylaws provide for the indemnification of our directors and officers to the fullest extent permitted under the General Corporation Law of the State of Delaware. Section 102(b)(7) of the General Corporation Law of the State of Delaware permits a corporation to provide in its certificate of incorporation that a director or officer of the corporation shall not be personally liable to the corporation or its stockholders for monetary damages for breach of fiduciary duties as a director or officer, except for liability for any:

Our amended and restated certificate of incorporation, as amended, includes such a provision with respect to our directors. Expenses incurred by any officer or director in defending any such action, suit or proceeding in advance

II-1 of its final disposition will be paid by us upon delivery to us of an undertaking, by or on behalf of such director or officer, to repay all amounts so advanced if it shall ultimately be determined that such director or officer is not entitled to be indemnified by us.

Section 174 of the General Corporation Law of the State of Delaware provides, among other things, that a director who willfully or negligently approves of an unlawful payment of dividends or an unlawful stock purchase or redemption, may be held liable for such actions. A director who was either absent when the unlawful actions were approved or dissented at the time may avoid liability by causing his or her dissent to such actions to be entered in the books containing minutes of the meetings of the board of directors at the time such action occurred or immediately after such absent director receives notice of the unlawful acts.

As permitted by the General Corporation Law of the State of Delaware, we have entered, and continue to enter, into separate indemnity agreements with each of our directors and executive officers that require us to indemnify such persons against any and all costs and expenses (including attorneys’, witness or other professional fees) actually and reasonably incurred by such persons in connection with any action, suit or proceeding (including derivative actions), whether actual or threatened, to which any such person may be made a party by reason of the fact that such person is or was a director or officer or is or was acting or serving as an officer, director, employee or agent of ours or any of our affiliated enterprises. Under these agreements, we are not required to provide indemnification for certain matters, including:

The indemnification agreements also set forth certain procedures that will apply in the event of a claim for indemnification thereunder.

We have an insurance policy in place that covers our officers and directors with respect to certain liabilities, including liabilities arising under the Securities Act or otherwise.

Pursuant to certain underwriting agreements we may enter, the underwriters are obligated, under some circumstances, to indemnify our directors, officers and controlling persons against specified liabilities, including liabilities under the Securities Act.

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The following list sets forth information as to all unregistered securities we have sold since January 1, 2022 through the date of the prospectus that is a part of this registration statement:

April 2023 Private Placement

On April 13, 2023, we entered into a Purchase Agreement (the “April 2023 Purchase Agreement”) with David Barker (“April 2023 Purchaser”), the Chair of the Company’s board of directors, pursuant to which we agreed to issue and sell one share of the Company’s Series A Preferred Stock, par value $0.0001 per share, to the April 2023 Purchaser for a purchase price of $100.00. The closing of the sale and purchase of the share of Series A Preferred was completed on April 13, 2023. The April 2023 Purchaser is an “accredited investor” and the offer and sale of the share of Series A Preferred was exempt from registration under Section 4(a)(2) of the Securities Act.

October 2023 Private Placement

On October 11, 2023, we entered into a securities purchase agreement (the “October 2023 Purchase Agreement”) with High Trail Special Situations LLC (the “October 2023 Purchaser”) pursuant to which we issued to the October 2023 Purchaser: (i) in a registered offering (the “October 2023 Registered Offering”) (a) $45.0 million aggregate principal amount of senior secured convertible notes due 2025 (the “Registered Notes”) initially convertible into 261,894 shares of our common stock (as adjusted for the reverse stock split) and (b) warrants to purchase up to 361,011 shares of our common stock (as adjusted for the reverse stock split) (the “Registered Warrants”); and (ii) in a concurrent private placement (the “October 2023 Private Placement”), $35.0 million aggregate principal amount of senior secured convertible notes due 2025 initially convertible at a price of $171.60 (as adjusted for the reverse stock split) into 203,696 shares of our common stock (as adjusted for the reverse stock split) (the “Private Placement Notes” and together with the Registered Notes, the “Notes”). The October 2023 Registered Offering and the October 2023 Private Placement closed on October 13, 2023.

Pursuant to the October 2023 Purchase Agreement, we also granted the October 2023 Purchaser an option to purchase up to an additional $25.0 million aggregate principal amount of Private Placement Notes initially convertible into 145,497 shares of our common stock (as adjusted for the reverse stock split) (the “Subsequently Purchased Notes”) and warrants (the “Private Placement Warrants” and together with the Registered Warrants, the “October 2023 Warrants”) to purchase up to 112,816 shares of our common stock (as adjusted for the reverse stock split) in a subsequent private placement on the same terms as the October 2023 Notes and the Registered Warrants (any such subsequent private placement, a “Subsequent Private Placement”).

Cowen and Company, LLC and Stifel, Nicolaus & Company, Incorporated acted as co-lead placement agents and BTIG, LLC as placement agent (together, the “Placement Agents”) for the sale of the October 2023 Notes and the October 2023 Warrants, pursuant to a placement agent agreement, by and between us and the Placement Agents dated October 11, 2023. We paid the Placement Agents a cash fee equal to $2.7 million and agreed to pay a cash fee equal to 6.0% of the gross proceeds from the sale of any Subsequent Private Placement.

The Private Placement Notes and the shares of common stock underlying the Private Placement Notes were issued in reliance upon Rule 506 of Regulation D promulgated under the Securities Act, as a transaction not requiring registration under the Securities Act and was made without general solicitation or advertising. Pursuant to the October 2023 Purchase Agreement, the October 2023 Purchaser represented that it is an accredited investor and that it is acquiring the securities for investment purposes only and not with a view to any resale, distribution or other disposition of such securities in violation of the Securities Act.

May 2024 Private Placement

On May 24, 2024, we entered into a securities purchase agreement (the “May 2024 Purchase Agreement”) with certain accredited investors (the “May 2024 Investors”) and JGB Collateral LLC, as collateral agent, pursuant to which we issued to the May 2024 Investors in a private placement (the “May 2024 Private Placement”): (i) 37,500 shares of our common stock (as adjusted for the reverse stock split) (the “May 2024 Shares”), and (ii) Senior Secured Convertible Debentures in the aggregate principal amount of $20,000,000 (the “May 2024 Debentures”), for an aggregate purchase price of $18,000,000.

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Canaccord Genuity LLC (“Canaccord”) acted as the exclusive placement agent for the May 2024 Private Placement, which was conducted on a “reasonable best efforts” basis, pursuant to a placement agent agreement (the “Placement Agent Agreement”), dated May 24, 2024, by and between us and Canaccord. Pursuant to the Placement Agent Agreement, we paid Canaccord a cash fee equal to 6.0% of the of the aggregate face value of the May 2024 Debentures issued in the May 2024 Private Placement. In addition, we agreed to reimburse Canaccord for any out-of-pocket expenses incurred by Canaccord in connection with the May 2024 Private Placement not to exceed $75,000. The May 2024 Private Placement closed on May 24, 2024, and the Company received net proceeds of approximately $16.6 million after payment of placement agent fees, and other offering expenses.

The May 2024 Shares and the May 2024 Debentures were issued in reliance upon Rule 506 of Regulation D promulgated under the Securities Act, as a transaction not requiring registration under the Securities Act and was made without general solicitation or advertising. Pursuant to the May 2024 Purchase Agreement, the May 2024 Investors each represented that it is an accredited investor and that it is acquiring the securities for investment purposes only and not with a view to any resale, distribution or other disposition of such securities in violation of the Securities Act.

December 2024 Settlement Agreement and Amendment to Securities Purchase Agreement

On December 31, 2024, we entered into a settlement agreement and amendment (the “Amendment”) relating to our outstanding May 2024 Debentures. Pursuant to the Amendment, the conversion price to convert outstanding principal amounts of the May 2024 Debentures to shares of our common stock was adjusted. As a result of this conversion price adjustment, the $15,000,000 outstanding aggregate principal amount of the May 2024 Debentures would be convertible into 925,925 shares of common stock (as adjusted for the reverse stock split), of which 759,259 shares (as adjusted for the reverse stock split) were not previously registered under the Securities Act (the “Unregistered Conversion Shares”). As consideration for the Amendment, we issued the May 2024 Investors 83,333 shares of our common stock (as adjusted for the reverse stock split) (the “New Shares” and, together with the Unregistered Conversion Shares, the “Shares”) and to forbear from issuing a redemption notice under the May 2024 Debentures to the May 2024 Investors prior to July 31, 2025.

The Shares were issued in a transaction not involving public offering under Section 4(a)(2) of the Securities Act as a transaction not requiring registration under the Securities Act and was made without general solicitation or advertising. Pursuant to the Amendment, the May 2024 Investors each represented that it is an accredited investor and that it is acquiring the Shares for investment purposes only and not with a view to any resale, distribution or other disposition of such Shares in violation of the Securities Act.

July 2024 Private Placement

On July 4, 2024, we entered into a securities purchase agreement (the “July 2024 Purchase Agreement”) with certain institutional investors (the “Purchasers”), pursuant to which we issued to the Purchasers: (i) in a registered direct offering priced at-the-market consistent with the rules of the Nasdaq Stock Market, (a) an aggregate of 195,000 shares of our common stock (as adjusted for the reverse stock split) and (b) pre-funded warrants to purchase up to an aggregate of 96,885 shares of our common stock (as adjusted for the reverse stock split); and (ii) in a concurrent private placement, Series A warrants to purchase up to an aggregate of 291,885 shares of our common stock (as adjusted for the reverse stock split) (the “Series A Warrants”) and Series B warrants to purchase up to an aggregate of 291,885 shares of our common stock (as adjusted for the reverse stock split) (the “Series B Warrants”, and together with the Series A Warrants, the “July 2024 Purchase Warrants”). Each share of common stock and each pre-funded warrant sold pursuant to the July 2024 Purchase Agreement was accompanied by one Series A Warrant and one Series B Warrant. The combined purchase price of each share of common stock and accompanying July 2024 Purchase Warrants was $34.260 per share (as adjusted for the reverse stock split). The combined purchase price of each pre-funded warrant and accompanying July 2024 Purchase Warrants was $34.259 (as adjusted for the reverse stock split).

H.C. Wainwright & Co., LLC (“Wainwright”) acted as the exclusive placement agent for the Company on a “reasonable best efforts” basis in connection with the transactions pursuant to an engagement letter (the “Engagement Letter”), by and between us and Wainwright. Pursuant to the Engagement Letter, the Company paid Wainwright an aggregate cash fee equal to 6.0% of the gross proceeds received in the Offering and for certain expenses incurred by Wainwright in connection with the offering.

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We received gross proceeds of approximately $10.0 million (excluding up to $20.0 million of aggregate gross proceeds that may be received in the future upon the cash exercise of the July 2024 Purchase Warrants), before deducting placement agent fees and other offering expenses payable by the Company. We received net proceeds of $9.3 million after deducting placement agent fees and other offering expenses of $0.7 million payable by us.

The July 2024 Purchase Warrants were issued in reliance upon an exemption from the registration requirements under the Securities Act afforded by Section 4(a)(2) thereof and/or Rule 506(b) of Regulation D promulgated thereunder.

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provided, however, that the undertakings set forth in paragraphs (a)(1)(i), (a)(1)(ii) and (a)(1)(iii) above do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in reports filed with or furnished to the SEC by the registrant pursuant to section 13 or section 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in this registration statement or are contained in a form of prospectus filed pursuant to Rule 424(b) that is part of this registration statement.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the registrant has duly caused this registration statement to be signed on its behalf by the undersigned, thereunto duly authorized in the City of San Diego, State of California, on September 11, 2025.

POWER OF ATTORNEY

We, the undersigned officers and directors of Bionano Genomics Inc., hereby severally constitute and appoint R. Erik Holmlin, Ph.D. and Mark Adamchak, and each of them singly (with full power to each of them to act alone), to sign any and all amendments (including post-effective amendments) to this registration statement (or any other registration statement for the same offering that is to be effective upon filing pursuant to Rule 462(b) under the Securities Act of 1933), and to file the same, with all exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite or necessary to be done in and about the premises, as full to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents or any of them, or their or his substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this registration statement has been signed by the following persons on September 11, 2025 in the capacities indicated.

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