UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO § 240.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO

§ 240.13d-2(a)

Under the Securities Exchange Act of 1934

(Amendment No. 3)¹

¹ The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. ¨

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

Page 7 of 10 Pages

This Amendment No. 3 (this “Amendment”) amends and supplements the Schedule 13D filed on November 4, 2013 (the “Filing”), by the Reporting Persons, as defined therein, relating to the common stock, par value $0.001 per share, of Crossroads Systems, Inc., a Delaware corporation (the “Company”). Information reported in the Filing remains in effect except to the extent that it is amended, restated or superseded by information contained in this Amendment. Capitalized terms used but not defined in this Amendment have the respective meanings set forth in the Filing.

Item 3 is hereby amended by deleting Item 3 of the Filing in its entirety and replacing it with the following:

The Shares purchased by Lone Star Value LP were purchased with working capital (which may, at any given time, include margin loans made by brokerage firms in the ordinary course of business). 914,700 of the Shares were purchased in open market purchases. 1,288,352 of the Shares were purchased in a private placement by the Company, pursuant to a Securities Purchase Agreement as described in Item 6 below. The aggregate purchase price of the 2,203,052 shares of Common Stock beneficially owned by Lone Star Value LP is approximately $3,822,166, excluding brokerage commissions.

Item 4 is hereby amended by deleting Item 3 of the Filing in its entirety and replacing it with the following:

The Reporting Persons expect that any acquisition of shares of Common Stock will be for investment purposes. Mr. Eberwein is Chairman of the Board of Directors of the Company.

The Reporting Persons may review Lone Star Value LP’s investment in the Company on a continuing basis and any of the Reporting Persons may in the future engage in discussions with management, the board of directors, other stockholders and other relevant parties concerning the business, operations, board composition, management, strategy and future plans of the Company. Although no Reporting Person has any specific plan or proposal to purchase or sell shares of Common Stock, depending on various factors including, without limitation, the results of any such discussions, the Company’s financial position and business strategy, price levels of the Shares, conditions in the securities market and general economic and industry conditions, the Reporting Persons may in the future take such actions with respect to their investment in the Company as they deem appropriate including, without limitation, purchasing additional shares or selling some or all of their Shares or engaging in any hedging or similar transactions with respect to the Shares. Except as set forth above, the Reporting Persons have no present plans or intentions that would result in or relate to any of the matters described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

The description of each of the Purchase Plan, the Securities Purchase Agreement and the Registration Rights Agreement in Item 6 below is incorporated herein by reference.

Item 5 is hereby amended by deleting Item 5 of the Filing in its entirety and replacing it with the following:

The aggregate percentage of Shares reported owned by each person named herein is based upon 14,770,145 shares of Common Stock issued and outstanding, which is the sum of (i) 12,883,523, the total number reported outstanding as of March 31, 2014, as represented by the Company in the Securities Purchase Agreement, and (ii) 1,886,622, the total number of shares sold pursuant to the Securities Purchase Agreement.

The Reporting Persons (other than Mr. Eberwein) may be deemed to beneficially own an aggregate of 2,203,052 shares of Common Stock (the “Shares”). In addition to the shares held directly by Lone Star Value LP, Mr. Eberwein beneficially owns 18,151 options to purchase shares of Common Stock that were issued to Mr. Eberwein in connection with this service as a director of the Company.

The Shares beneficially owned by the Reporting Persons (other than Mr. Eberwein) represent approximately 14.9% of the outstanding shares of Common Stock. Mr. Eberwein beneficially owns approximately 15.0% of the outstanding shares of Common Stock.

Page 8 of 10 Pages

(a)                 2,203,052 shares of Common Stock are beneficially owned directly by Lone Star Value LP. Lone Star Value GP is the general partner of, and controls, Lone Star Value LP. Lone Star Management exercises contractual voting and investment control over securities held by Lone Star Value LP. Mr. Eberwein is the managing member of Lone Star Management and exercises indirect voting and investment control over these securities. By reason of these relationships, each Reporting Person may be deemed to share the power to vote or direct the vote and to dispose or direct the disposition of the Shares beneficially owned by such Reporting Person as indicated above.

Mr. Eberwein beneficially owns 18,151 options to purchase shares of Common Stock that were issued to Mr. Eberwein in connection with this service as a director of the Company.

Lone Star Value GP, Lone Star Management and Mr. Eberwein disclaim beneficial ownership of the Shares held directly by Lone Star Value LP. The filing of this Statement shall not be construed as an admission that any of the Reporting Persons share beneficial ownership for purposes of Section 13(d) of the Exchange Act.

(b)                 Other than the purchase of 1,288,352 Shares pursuant to the Securities Purchase Agreement described in Item 4 and Item 6, Lone Star Value LP has not made any additional transactions in the Shares during the past 60 days.

An aggregate of 2,203,052 shares of Common Stock, constituting approximately 14.9% of the outstanding shares of Common Stock, are reported in this Schedule 13D.

The Reporting Persons, as members of a “group” for the purposes of Section 13(d)(3) of the Securities Exchange Act of 1934, as amended, may be deemed the beneficial owner of the Shares directly owned by the other Reporting Person. Each Reporting Person disclaims beneficial ownership of such Shares except to the extent of his or its pecuniary interest therein.

(c)                 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 Shares.

(d)                 Not applicable.

Item 6 is hereby amended by deleting Item 6 of the Filing in its entirety and replacing it with the following:

On October 11, 2013, Lone Star Value LP entered into a stock purchase plan (the “Purchase Plan”) pursuant to Rule 10b5-1 of the Securities Exchange Act of 1934, as amended. Under the Purchase Plan, a broker dealer will make periodic purchases of up to an aggregate of 1,190,000 shares of Common Stock on behalf of Lone Star Value LP at prevailing market prices, subject to the terms of the Purchase Plan. This description of the Purchase Plan does not purport to be complete and is qualified in its entirety by the text of the Purchase Plan, a copy of which is attached as Exhibit 99.1 hereto and is incorporated herein by reference.

On November 4, 2013, the Reporting Persons entered into a Joint Filing Agreement in which the Reporting Persons agreed to the joint filing on behalf of each of them of statements on Schedule 13D with respect to securities of the Issuer, to the extent required by applicable law. A copy of this agreement is attached as Exhibit 99.2 hereto and is incorporated herein by reference.

On March 31, 2013, Lone Star Value LP entered into that certain Securities Purchase Agreement by and among the Company and the Buyers listed as parties thereto (the “Securities Purchase Agreement”). Pursuant to the Securities Purchase Agreement, Lone Star Value LP purchased in a private placement 1,886,622 Units (the “Units”). Each Unit consists of one share of the Common Stock and warrants to purchase one-half of a share of Common Stock (the “Warrants”), which become exercisable September 31, 2014. Each of the Company and the Investors made customary representations and warranties and the Purchase Agreement contains customary indemnification provisions.

Page 9 of 10 Pages

In connection with the Securities Purchase Agreement, on March 31, 2014, Lone Star Value LP, the Company and the Buyers under the Securities Purchase Agreement entered into a Registration Rights Agreement (the “Registration Rights Agreement”). Under the Registration Rights Agreement, the Company is required to prepare and file with the Securities and Exchange Commission (the “SEC”) a registration statement within 60 days after the closing date of the private placement of the shares issued pursuant to the Securities Purchase Agreement. The Company is obligated to use its reasonable best efforts to cause the Resale Registration Statement to be declared effective by the SEC by the 120th day after the date of the Securities Purchase Agreement. The Registration Rights Agreement also contains customary indemnification provisions.

The foregoing summaries of the Securities Purchase Agreement and the Registration Rights Agreement are not complete, and are qualified in their entirety by reference to the texts of the agreements attached as Exhibit 99.3 and Exhibit 99.4 hereto, respectively, and are each incorporated herein by reference.

Item 7 is hereby amended by deleting Item 7 of the Filing in its entirety and replacing it with the following:

Signatures

After reasonable inquiry and to the best of the knowledge and belief of the undersigned, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated: April 4, 2014