UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

Yandex N.V.

(Name of Issuer)

Class A Common Stock

(Title of Class of Securities)

N97284108

(CUSIP Number)

Mr. Igmar den Heijer, Strawinskylaan 411, WTC Tower A 4^th fl., 1077 XX Amsterdam, the Netherlands

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

March 16, 2015

(Date of Event Which Requires Filing of This Statement)

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. ¨

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

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 (however, see the Notes).

option that is currently exercisable. Excludes options to purchase 1,750 Class A shares that are not exercisable within 60 days of the date hereof. The options were granted by Yandex effective on the closing of Yandex’s initial public offering in May 2011, and vest over a four year period. Each Class B Share is entitled to ten votes per share, and each Class A Share is entitled to one vote per share. The Class A Shares and Class B Shares are held of record by BC&B Holdings B.V., a company incorporated under the laws of the Netherlands (“BC&B”). BC&B is 100% owned by BC&B Coöperatief U.A., a cooperative association with exclusion of liability incorporated under the laws of the Netherlands (“BC&B Coop” or the “Reporting Person”). See the Explanatory Note to Exhibit A hereto.

Explanatory Note:

This Amendment No. 3 to Schedule 13D (the “Amendment”) is filed by BC&B Coöperatief U.A., a cooperative association with exclusion of liability incorporated under the laws of the Netherlands (“BC&B Coop” or the “Reporting Person”), to amend the Schedule 13D related to the Class A Shares of Yandex N.V. (“Yandex”) previously filed by the Reporting Person with the Securities and Exchange Commission on March 4, 2014 (the “Schedule 13D”) and as subsequently amended. The Class A Shares reported in the Schedule 13D are held of record by BC&B Holdings B.V., a company incorporated under the laws of the Netherlands (“BC&B”). See the Explanatory Note to Exhibit A, which is incorporated by reference herein.

Each capitalized term used and not defined herein shall have the meaning assigned to such term in the Schedule 13D. Except as otherwise provided herein, each Item of the Schedule 13D remains unchanged.

Item 4 of the Schedule 13D is hereby amended and restated in its entirety as follows:

The acquisition of beneficial ownership of the Class A Shares reported in this Schedule 13D by BC&B Coop from Strickland was the result of an internal restructuring which did not change the ultimate beneficial ownership of the shares. See the Explanatory Note to the Schedule 13D, which is incorporated herein by reference.

(a) BC&B Coop and, to its knowledge, the other persons listed on Schedule A hereto, may seek to sell the Class A Shares it or they beneficially own in the ordinary course of its or their business.

On June 16, 2014, BC&B entered into the Sales Plan, dated June 16, 2014 (the “10b5-1 Sales Plan”), between BC&B Holdings B.V., a company incorporated under the laws of the Netherlands (“BC&B”), and Morgan Stanley & Co. LLC (“Morgan Stanley”), pursuant to which Morgan Stanley was authorized to sell up to 19,989,591 Class A Shares through June 5, 2015, and amended the Plan on August 28, 2014. The 10b5-1 Sales Plan was further amended on March 16, 2015 (as amended, the “Amended 10b5-1 Sales Plan”) to extend the period under which sales can be made to the earliest of June 30, 2016, the date that the aggregate number of share sold pursuant to the Amended 10b5-1 Sales Plan after the date of the Amendment reaches 14,701,048 Class A shares and the occurrence of other termination events specified in the Plan, as well as to change the price and volume limitations under which sales may be made under the plan. The Amended 10b5-1 Sales Plan is intended to comply with Rule 10b5-1 under the Securities Exchange Act of 1934. Transactions under the Amended 10b5-1 Sales Plan will be subject to certain price and volume restrictions and other conditions under the Amended 10b5-1 Sales Plan, and may be terminated by BC&B at any time. The form of the Amended 10b5-1 Sales Plan is being filed as an exhibit hereto and the foregoing description of the Amended 10b5-1 Sales Plan is qualified in its entirety by reference thereto.

BC&B has agreed to distribute Class A Shares to Caldwell Associated Inc., a company associated with Elena Ivashentseva, a senior partner at Baring Vostok Capital Partners Limited, a Russian private equity firm, and a director of Yandex, in lieu of all or a portion of amounts otherwise due to Caldwell in respect of Baring Vostok Private Equity Fund II.

(f) BC&B Coop, and the other persons listed on Schedule A hereto, may engage in discussions with management, Yandex’s board of directors, other Yandex shareholders and other relevant parties concerning the business, operations, board composition, management, strategy and future plans of Yandex. Pursuant to the Amended and Restated Shareholders Agreement (as defined in Item 6 of this Schedule 13D), BC&B and the other shareholders that are parties to the Amended and Restated Shareholders Agreement, have agreed to vote the shares held by them in favor of electing or re-electing those persons nominated by Yandex’s board of directors for election or re-election as a director at any general meeting of Yandex shareholders.

One of the members of Yandex’s board of directors, Elena Ivashentseva, is a senior partner at Baring Vostok Capital Partners Limited, a Russian private equity firm. Each of Ms. Ivashentseva and Baring Vostok Capital Partners Limited disclaims beneficial interest in the securities held by the Reporting Person.

As a result of these activities, and subject to the limitations set forth in the Amended and Restated Shareholders Agreement and the Amended and Restated Registration Rights Agreement (as defined in Item 6 of this Schedule 13D), BC&B Coop may suggest or take a position with respect to potential changes in the business, operations, management or capital structure of Yandex. Such suggestions or positions may include one or more plans or proposals that relate to or would result in any of the actions required to be reported herein.

To the knowledge of BC&B Coop, each of the persons listed on Schedule A hereto may make the same evaluation and reserve the same rights.

Item 5 of the Schedule 13D is hereby amended by amending and restating Exhibit A hereto, which is incorporated herein by reference.

Item 6 is hereby amended and supplemented to add the following to the end thereof:

Amended 10b5-1 Sales Plan

On March 16, 2015 BC&B and Morgan Stanley entered into the Amended 10b5-1 Sales Plan. The information set forth in Item 4 above is hereby incorporated by reference into this Item 6. The information in this Item 6 is qualified in its entirety by reference to the Amended 10b5-1 Sales Plan, attached hereto as Exhibit 4, and is incorporated by reference herein.

Item 7 is hereby amended and supplemented by adding the following exhibit:

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

SCHEDULE A

Persons other than Individuals:

The entities listed above are investment funds or their related general partners or nominee or holding companies. The principal address of each such entity is 1 Royal Plaza, Royal Avenue, St Peter Port, Guernsey GY1 2HL.

Individuals:

The business address for each of the individuals listed above other than Mr. den Heijer is 1 Royal Plaza, Royal Avenue, St Peter Port, Guernsey GY1 2HL. The business address for Mr. den Heijer is WTC Tower A 4th floor, Strawinskylaan 411, 1077 XX Amsterdam, the Netherlands.

Each individual listed in the table above disclaims beneficial ownership of the Class A Shares that may be beneficially owned by each of the other entities and individuals listed in this Schedule A and this report shall not be construed as an admission that such persons are the beneficial owner of such securities.

EXHIBIT A

Item 5(a)(b) – Interest in Securities of the Issuer

Explanatory Note:

The Class A Shares reported in this Schedule 13D are held of record by BC&B Holdings B.V., a company incorporated under the laws of the Netherlands (“BC&B”). BC&B Coöperatief U.A., a cooperative association with exclusion of liability incorporated under the laws of the Netherlands (“BC&B Coop” or the “Reporting Person”), holds 100% of the share capital of BC&B. 52.35% of the share capital of BC&B Coop is held by Chouet Nominees Limited (“CHNL”), 23.89% of the share capital of BC&B Coop is held by Baring Vostok Nominees Limited (“BVNL”) and 23.76% of the share capital of BC&B Coop is held by Dehus Dolmen Nominees Limited (“DDNL”). Through their ownership of BC&B Coop, therefore, CHNL has the right to control the voting and disposition of 822,172 Class A shares, 13,742 Class A shares that are subject to an option that is currently exercisable and 6,961,378 Class B shares held by BC&B; BVNL has the right to control the voting and disposition of 375,160 Class A shares, 6,271 Class A shares that are subject to an option that is currently exercisable and 3,176,497 Class B shares held by BC&B; and DDNL has the right to control the voting and disposition of 373,183 Class A Shares, 6,237 Class A shares that are subject to an option that is currently exercisable and 3,159,761 Class B shares held by BC&B. BVNL, DDNL and CHNL disclaim beneficial ownership of the shares held by BC&B except to the extent of its pecuniary interest therein and this report shall not be construed as an admission that such persons are the beneficial owner of such securities. See Note 1 to this Schedule 13D, which is incorporated herein by reference.

Each of BVNL, DDNL and CHNL may be deemed members of a group with BC&B Coop and BC&B by reason of the relationships described above. Such persons may also be deemed members of a group with each of the other persons listed in the table above by reason of the relationships described below. Each such person disclaims membership in such group and this report shall not be construed as an admission that such persons are members of a group.

CHNL is a limited liability company that acts as nominee holding company for Baring Vostok Private Equity Fund (“BVPEF”). Baring Vostok Fund Managers Limited (“BVFML”) is the General Partner to Baring Vostok Fund (GP) L.P. who in turn is the General Partner to each of the Limited Partnerships comprising BVPEF. Each of BVFML and Baring Vostok Fund (GP) L.P. disclaim beneficial ownership of the shares beneficially owned by CHNL and BVPEF except to the extent of its pecuniary interest therein and this report shall not be construed as an admission that such persons are the beneficial owner of such securities.

BVNL is a limited liability company that acts as nominee holding company for Baring Vostok Private Equity Fund III (“BVPEFIII”). Baring Vostok Fund III Managers Limited (“BVFIIIML”) is the General Partner to Baring Vostok Fund III (GP) L.P. who in turn is the General Partner to each of the Limited Partnerships comprising BVPEFIII. Each of BVFIIIML and Baring Vostok Fund III (GP) L.P. disclaim beneficial ownership of the shares beneficially owned by BVNL and BVPEFIII except to the extent of its pecuniary interest therein and this report shall not be construed as an admission that such persons are the beneficial owner of such securities.

DDNL is a limited liability company that acts as nominee holding company for Baring Vostok Private Equity Fund IV (“BVPEFIV”). Baring Vostok Fund IV Managers Limited (“BVFIVML”) is the General Partner to Baring Vostok Fund IV (GP) L.P. who in turn is the General Partner to each of the Limited Partnerships comprising BVPEFIV. Each of BVFIVML and Baring Vostok Fund IV (GP) L.P. disclaim beneficial ownership of the shares beneficially owned by DDNL and BVPEFIV except to the extent of its pecuniary interest therein and this report shall not be construed as an admission that such persons are the beneficial owner of such securities.

Each of BVFML, BVFIIIML and BVFIVML (together the “General Partners”) are owned by Baring Vostok Manager Holding Limited (Guernsey) (“BVMHL”). BVMHL disclaims beneficial ownership of the shares beneficially owned or deemed beneficially owned by each of the other persons listed in the table above except to the extent of its pecuniary interest therein and this report shall not be construed as an admission that such person is the beneficial owner of such securities.

Voting and investment power over the investments held by each of the limited partnerships in the Baring Vostok funds is exercised by each fund’s respective General Partner. Baring Vostok Capital Partners Limited, as investment advisor to the Baring Vostok funds, has no voting or investment control over the Baring Vostok funds. The General Partners make decisions based on recommendations of investment committees appointed in respect of BVPEF, BVPEFIII and BVPEFIV. Baring Vostok Capital Partners Limited disclaims beneficial interest in the securities held by the Reporting Person and the other persons listed on the table above.

The beneficial ownership of shares by the persons listed in the table above, other than BC&B Coop, are not the subject of this Schedule 13D and such persons are accordingly not included as Reporting Persons. Such beneficial ownership is reported on the Schedule 13G initially filed by such persons on February 14, 2012, as subsequently amended.

Exhibit 99.5

Execution Version

Amendment No. 2 to Sales Plan

Amendment No. 2, dated March 16, 2015 (this “Amendment No. 2”), to the Sales Plan dated June 16, 2014, as amended on August 28, 2014 (the “Sales Plan”) between BC&B Holdings B.V., a company incorporated under the laws of the Netherlands (“Seller”), and Morgan Stanley & Co. LLC (“Morgan Stanley”), acting as agent for Seller, for the purpose of establishing a trading plan that complies with the requirements of Rule 10b5-1(c)(1) under the Securities Exchange Act of 1934, as amended, for the disposition of a portion of the Seller’s holdings of Class A Shares (including Class A Shares issued upon conversion of the Seller’s holdings of Class B Shares) (the “Stock”) of Yandex N.V. Terms used without definition herein shall have the respective meanings given in the Sales Plan.

1. Schedule A to the Sales Plan is hereby amended and replaced in its entirety with Schedule A attached hereto, and from the date hereof references to the “Minimum Sale Price” and “Daily Sale Amount” shall be determined and calculated in accordance with such Schedule A attached hereto.

2. Paragraph B.2 is hereby amended in its entirety to read as follows: “Morgan Stanley is authorized to begin selling Stock pursuant to this Sales Plan on July 17, 2014 (the “Commencement Date”) and shall cease selling Stock on the earliest to occur of (i) the date on which Morgan Stanley is required to suspend or terminate sales pursuant to paragraph C.1 below, (ii) the date on which Morgan Stanley receives notice of the commencement or impending commencement of any proceedings in respect of or triggered by Seller’s bankruptcy or insolvency (iii) June 30, 2016 and (iv) the date that the aggregate number of shares of Stock sold pursuant to this Sales Plan after the date of this Amendment No. 2 reaches 14,701,048 Class A shares (the “Total Sale Amount”) (such period, the “Plan Period”).

The Seller hereby certifies that the representations and warranties of Seller contained in the Sales Plan are true at and as of the date hereof as if made at and as of such date.

1. Upon execution of this Amendment No. 2, the Sales Plan shall be, and be deemed to be, modified and amended in accordance herewith and the respective rights, limitations, obligations and duties of the parties thereto shall hereafter be determined and exercised subject in all respects to such modifications and amendments. Except as expressly modified and amended by this Amendment No. 2, the Sales Plan is in all respects ratified and confirmed, and all the terms, provisions and conditions thereof shall be and remain in full force and effect.

2. This Amendment No. 2 may be signed in any number of counterparts, each of which shall be an original, with the same effect as if the signatures thereto and hereto were upon the same instrument.

3. This Amendment No. 2 shall be governed by and construed in accordance with the internal laws of the State of New York and may be modified or amended only by a writing signed by the parties hereto.

2

IN WITNESS WHEREOF, the undersigned have signed this Amendment No. 2 as of the date first written above.