Filed Pursuant to Rule 424(b)(3)

Registration No. 333-239971

Prospectus Supplement No. 4

(to Prospectus dated July 23, 2020)

BIONTECH SE

Rights Offering for up to 7,505,596 Ordinary Shares Including Ordinary Shares Represented by American Depositary Shares

This Prospectus Supplement No. 4 supplements information contained in our prospectus, dated July 23, 2020, relating to the offering to holders of our ordinary shares and American Depositary Shares, or ADSs, representing our ordinary shares, of rights to subscribe for up to an aggregate of 7,505,596 new ordinary shares and new ADSs representing our ordinary shares.

This prospectus supplement is being filed to update, amend and supplement the information previously included in the prospectus with our quarterly report for the three and six months ended June 30, 2020, which is set forth below. This prospectus supplement should be read in conjunction with the prospectus dated July 23, 2020. To the extent there is a discrepancy between the information contained in this prospectus supplement and the information in the prospectus, the information contained herein supersedes and replaces such conflicting information.

You should carefully consider whether or not to exercise your subscription rights before the expiration of the rights offering at one minute after 11:59 p.m. (Mainz, Germany time) on August 14, 2020 (for ordinary share rights) or 12:01 a.m. (New York City time) on August 14, 2020 (for ADS rights). All exercises of rights to subscribe for new ADSs are irrevocable. Neither we, our supervisory board, the dealer-managers nor the subscription agents are making a recommendation regarding your exercise of the subscription rights.

Investing in our ordinary shares and ADSs representing our ordinary shares involves a high degree of risk. See “Risk Factors” beginning on page 22 of the prospectus, together with all of the other information contained in the prospectus and in our filings with the Securities and Exchange Commission that we have incorporated by reference in the prospectus.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

The date of this Prospectus Supplement No. 4 is August 11, 2020.

BioNTech SE

Quarterly Report for the Three and Six Months ended June 30, 2020

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BioNTech SE

Quarterly Report for the Three and Six Months ended June 30, 2020

Index

Interim Condensed Consolidated Financial Statements

Operating and Financial Review and Prospects

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Interim Condensed Consolidated Financial Statements

Interim Condensed Consolidated Statements of Financial Position

The accompanying notes form an integral part of these interim condensed consolidated financial statements.

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Interim Condensed Consolidated Statements of Operations

* Foreign exchange differences on a cumulative basis are either shown as finance income or expenses and might switch between those two positions during the year-to-date reporting periods.

** Numbers of shares for calculating the earnings per share for the three and six months ended June 30, 2019 have been adjusted to reflect capital increase due to 1:18 share split which occurred on September 18, 2019.

The accompanying notes form an integral part of these interim consolidated financial statements.

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Interim Condensed Consolidated Statements of Comprehensive Loss

The accompanying notes form an integral part of these interim condensed consolidated financial statements.

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Interim Condensed Consolidated Statements of Changes in Stockholders’ Equity

* Numbers have been adjusted to reflect capital increase due to 1:18 share split which occurred on September 18, 2019.

The accompanying notes form an integral part of these interim condensed consolidated financial statements.

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Interim Condensed Consolidated Statements of Cash Flows

The accompanying notes form an integral part of these interim condensed consolidated financial statements.

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Selected Explanatory Notes to the Interim Condensed Consolidated Financial Statements

BioNTech SE is a limited company incorporated and domiciled in Germany. American Depositary Shares (ADS) representing BioNTech’s shares have been publicly traded on the Nasdaq Global Select Market since October 10, 2019. The registered office is located in Mainz, An der Goldgrube 12, 55131 Germany. The accompanying International Financial Reporting Standards, or IFRS, unaudited interim condensed consolidated financial statements present the financial position and the results of operation of BioNTech SE and its subsidiaries, hereinafter also referred to as “BioNTech” or the “Group” and have been prepared on a going concern basis in accordance with the IFRS as issued by the International Accounting Standards Board, or IASB.

BioNTech combines decades of groundbreaking research in immunology, cutting-edge therapeutic platforms and a suite of patient profiling and bioinformatic tools to develop immunotherapies for cancer and other diseases. BioNTech leverages powerful new therapeutic mechanisms and exploits a diverse array of biological targets to harness the power of each patient’s immune system to address the unique molecular signature of each patient’s underlying disease. The breadth of BioNTech’s immunotherapy technologies and expertise has enabled the Group to develop therapies to address a range of rare and infectious diseases, and BioNTech has recently rapidly mobilized these with the aim of addressing the COVID-19 pandemic.

On May 6, 2020 BioNTech SE acquired Neon Therapeutics, Inc., Cambridge, Massachusetts, United States (formerly Nasdaq: NTGN), or Neon. Under the merger agreement by and among BioNTech, Neon and BioNTech’s wholly owned subsidiary, Endor Lights, Inc., New York, United States, Endor Lights, Inc. merged with and into Neon. The new subsidiary operates under the name BioNTech US Inc., a wholly owned subsidiary of BioNTech SE, and serves as BioNTech’s headquarters in the United States. All BioNTech entities are included in the Group’s unaudited interim condensed consolidated financial statements.

These unaudited interim condensed consolidated financial statements of the Group as of and for the three and six months ended June 30, 2020 were authorized for issuance in accordance with a resolution of the audit committee on August 10, 2020.

Basis of Preparation

These unaudited interim condensed consolidated financial statements as of and for the three and six months ended June 30, 2020 have been prepared in accordance with IAS 34 Interim Financial Reporting.

The unaudited interim condensed consolidated financial statements do not include all the information and disclosures required in the consolidated financial statements and should be read in conjunction with the Group’s consolidated financial statements as of and for the year ended December 31, 2019.

BioNTech prepares and presents its unaudited interim condensed consolidated financial statements in Euros. Due to rounding, numbers presented throughout this document may not add up precisely to the totals provided and percentages may not precisely reflect the absolute figures.

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Significant Accounting Policies

The accounting policies adopted in the preparation of the unaudited interim condensed consolidated financial statements are consistent with those followed in the preparation of the Group’s consolidated financial statements for the year ended December 31, 2019. The standards applied for the first time as of January 1, 2020, as disclosed in the notes to the consolidated financial statements as of December 31, 2019, had no impact on the unaudited interim condensed consolidated financial statements of the Group as of June 30, 2020.

Impact of COVID-19

On March 11, 2020, the World Health Organization declared the outbreak of COVID-19 as a pandemic, which continues to spread throughout the United States, the European Union and around the world.

In response, BioNTech’s BNT162 program is evaluating at least four experimental vaccines aimed at preventing COVID-19 infection. As part of the program, BioNTech executed two strategic collaborations with large pharmaceutical companies to globally develop BioNTech’s vaccine candidates and supply an approved vaccine globally. BioNTech and Pfizer Inc. (NYSE: PFE), or Pfizer, aim to accelerate the development of BNT162 worldwide, excluding China, which is covered by BioNTech’s strategic alliance with Shanghai Fosun Pharmaceutical (Group) Co., Ltd (Stock Symbol: 600196.SH, 02196.HK), or Fosun Pharma.

As BioNTech advances its clinical programs, it is in close contact with its principal investigators and clinical sites, which are located in jurisdictions affected by the COVID-19 pandemic, and is assessing the impact of the COVID-19 pandemic on its clinical trials, expected timelines and costs on an ongoing basis. In light of recent developments relating to the COVID-19 pandemic, the primary focus of healthcare providers and hospitals remains on fighting the novel coronavirus. BioNTech has also modified its business practices, in response to the spread of COVID-19, including restricting employee travel, developing social distancing plans for employees and cancelling physical participation in meetings, events and conferences. In addition, for certain earlier stage programs, including BNT141 and BNT142 (RiboMabs), BNT151 and BNT152/153 (RiboCytokines), BNT161 (Influenza), BNT171 (Rare Disease) and BNT411 (TLR7), BioNTech has delayed commencement of trials, experienced slowed patient enrollment or experienced other delays as a result of the COVID-19 pandemic. This partial disruption, even temporary, may severely impact BioNTech’s operations and overall business by delaying the progress of its clinical trials and preclinical studies. Such factors were evaluated and considered carefully when preparing these unaudited interim condensed consolidated financial statements. BioNTech will continue to evaluate potential effects of the COVID-19 pandemic and will provide updates as appropriate.

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For the three and six months ended June 30, 2020 and 2019, respectively, the following tables present revenue and operating results for the Group’s operating segments consistent with the presentation in the notes to the consolidated financial statements as of December 31, 2019:

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The segments are managed based on external sales and operating profit/loss, which represents the operating profit/loss incurred within each segment. Segment figures are reported consolidated, which reflects the way management steers the business.

BioNTech’s internal reporting is generally in accordance with IFRS and in line with the Group’s accounting policies, except for minor deviations in classification between cost of sales and research and development cost. Whenever revenues are attributable to different segments, these revenues are split based on the cost incurred. Internal overhead costs are allocated to segments based on revenues when

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they are directly attributable to a service rendered. Sales and marketing expenses, general and administrative expenses and other results that are not directly attributable to one of the segments are allocated to Business Service.

In order to reconcile the segment figures to the Group’s unaudited interim condensed consolidated financial statements, some of the research and development expenses are reclassified to cost of sales.

Revenue at BioNTech is differentiated between revenues resulting from collaboration and license agreements and revenues from other sales transactions. The Company collaborates with pharmaceutical and healthcare companies and several global academic collaborators. During the three and six months ended June 30, 2020, revenue generated from the Genentech, Inc., or Genentech, and Pfizer collaboration agreements each represented more than 10% of BioNTech’s overall revenue resulting from collaboration and license agreements. Revenues were partly recorded in the Clinical and the Manufacturing segment and, with respect to Pfizer, in the Technology Platform segment as well. During the three months ended June 30, 2019, only revenue generated from the Genentech collaboration agreement represented more than 10% of BioNTech’s overall revenue from collaboration and license agreements. Revenues were partly recorded in the Clinical as well as the Manufacturing segment. During the six months ended June 30, 2019, revenue generated from the Genentech and Pfizer collaboration agreements each represented more than 10% of BioNTech’s overall revenue from collaboration and license agreements and were recorded in the Clinical segment and, with respect to Genentech, in the Manufacturing segment. Total amounts of revenues from these collaboration and license agreements in the periods presented are disclosed in Note 4.

Revenues from other sales transactions are from the sale of medical products (e.g., peptides and retroviral vectors) for clinical supply. Research and development activities are managed on a worldwide basis while manufacturing facilities and sales offices are located and managed in Germany. External sales originate in Germany.

Disaggregated revenue information

Set out below is the disaggregation of the Group’s revenues from contracts with customers:

During the three and six months ended June 30, 2020, revenues from BioNTech’s two new collaboration agreements aimed at developing a COVID 19 vaccine were recognized for the first time.

On March 13, 2020, BioNTech entered into a collaboration and license agreement with Fosun Pharma. Fosun Pharma paid BioNTech a non-refundable upfront cash payment of k€901 (k$1,000) upon signing the agreement in addition to an equity investment of k€45,568 (k$50,000) (see Note 10 for the capital contribution). BioNTech is eligible to receive future milestone payments of up to k$84,000 for potential aggregate consideration of k$135,000.

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On April 9, 2020, BioNTech entered into a collaboration and license agreement with Pfizer. Pfizer agreed to pay BioNTech k€170,146 (k$185,000), including an equity investment of k€103,890 (k$113,000) (see Note 10 for the capital contribution) and a non-refundable upfront cash payment of k€66,256 (k$72,000) which were received in late April 2020 and May 2020, respectively. BioNTech is eligible to receive future milestone payments of up to k$563,000 for potential aggregate consideration of k$748,000. Pfizer and BioNTech share development costs equally. Initially, Pfizer will fund 100% of the development costs, and BioNTech will repay Pfizer its 50% share of these costs if success-based milestones are reached, or with proceeds generated from the commercialization of the vaccine, if approved. If the vaccine program is not successful or does not generate sufficient proceeds, BioNTech will not be required to pay back its 50% share of the development costs incurred.

During the three months ended March 31, 2020, k€444 of the upfront payment from Fosun Pharma was recognized as revenue during the three months ended March 31, 2020. The remaining k€457 was recognized as revenue during the three months ended June 30, 2020. During the three months ended June 30, 2020, revenue from Pfizer was initiated to be recognized from the non-refundable upfront cash payment which has a restricted purpose by being dedicated to activities to be performed under the collaboration and license agreement. Based on cost incurred, k€20,613 revenue was recognized of which k€14,258 were directly incurred by BioNTech and k€6,356 have been accrued based on BioNTech’s 50% share of the shared development costs incurred. As services are performed under a collaboration agreement, revenue recognition will be continued in future periods in accordance with our accounting policy as described in “—Critical Accounting Policies and Use of Estimates” and Note 2.3.4 to our consolidated financial statements included in our Annual Report on Form 20-F for the year ended December 31, 2019.

Product sales included within revenue from other sales transactions are displayed below:

BioNTech US Inc. (formerly Neon Therapeutics, Inc.)

On May 6, 2020, BioNTech acquired Neon, a biotechnology company developing novel neoantigen-based T-cell therapies (“the Merger”). Through the acquisition, BioNTech will be able to leverage Neon’s expertise in the development of neoantigen therapies, with both vaccine and T cell capabilities.

Based on the acquisition date share price, the aggregate value of the merger consideration was k€89,890 (k$97,144) financed by issuing 1,935,488 American Depositary Shares representing BioNTech’s ordinary shares as a stock transaction and including a de minimis cash consideration which was paid to settle Neon’s outstanding stock options.

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The provisional fair values and values in accordance with IFRS 3 of the identifiable net assets of BioNTech US Inc. as at the date of acquisition were as follows:

During the measurement period, further considerations will be made especially with respect to the recoverability of tax losses carried forward. This will potentially have an impact on the identifiable net assets and the respective goodwill.

The interim condensed consolidated statement of operations includes the result of BioNTech US since the acquisition date. From the date of acquisition through June 30. 2020, BioNTech US contributed k€7,353 to the operating loss in all biotech business unit operating segments of the Group, primarily in the Technology Platform segment. If the transaction had occurred at the beginning of the reporting period, k€38,643 would have contributed to the operating loss. This amount includes expenses resulting from the Merger and should not necessarily be considered representative of the future consolidated results of operations or financial condition on a consolidated basis. From the date of acquisition, BioNTech US did not generate any revenue and no revenue would have been generated if the transaction had occurred at the beginning of the reporting period.

Provisional goodwill recognized is primarily attributable to the expected synergies and other benefits from combining two organizations with a common culture of pioneering translational science and a shared vision for the future of cancer immunotherapy as described above. The provisional goodwill resulting from the BioNTech US acquisition during the six months ended June 30, 2020 was provisionally allocated to the Technology Platform segment.

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Transaction costs of k€1,044 relating to the acquisition have been expensed and are included in the general and administrative expenses in the interim condensed consolidated statement of operations. To the extent that costs have already been invoiced and paid, k€1,007, they are included in cash flows used in operating activities in the interim condensed consolidated statement of cash flows. The attributable costs of the issuance of the shares of k€1,320 were recorded in equity as a deduction from the capital reserve and are included in cash flows from financing activities in the interim condensed consolidated statement of cash flows.

Lipocalyx GmbH

In December 2019, BioNTech Delivery Technologies GmbH (previously BioNTech Protein Therapeutics GmbH), or BioNTech Delivery Technologies, a wholly owned subsidiary of BioNTech SE, entered into an agreement to acquire all assets, employees and proprietary know-how of Lipocalyx GmbH, or Lipocalyx, and its related parties in exchange for a total consideration of cash at an amount of k€6,516 and additional contingent consideration estimated at the closing date of January 6, 2020 at an amount of k€572. The employees of Lipocalyx were transferred automatically to BioNTech Delivery Technologies with effect as of the closing date.

The Group acquired the assets of Lipocalyx and its related parties to combine the acquired technologies and the related know-how with already existing product candidates of the Group to improve their functionality and performance.

The final fair values of the identifiable net assets of Lipocalyx as at the date of acquisition were:

The interim condensed consolidated statement of operations includes the result of Lipocalyx since the acquisition date. From the date of acquisition, Lipocalyx contributed k€707 to operating loss in the Technology Platform business segment of the Group. From the date of acquisition through June 30, 2020, Lipocalyx generated k€176 in revenues. Given the timing of closing, the contribution to operating loss and revenues, if the transaction had occurred at the beginning of the reporting period, would not differ materially. Goodwill recognized is primarily attributed to the expected synergies and other benefits from combining the assets and activities of Lipocalyx with those of the Group. The goodwill resulting from the Lipocalyx acquisition during the six months ended June 30, 2020 was allocated to the Technology Platform segment.

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Transaction costs of k€17 relating to the acquisition have been expensed and are included in the general and administrative expenses in the interim condensed consolidated statement of operations and are included in cash flows used in operating activities in the interim condensed consolidated statement of cash flows.

The purchase agreement with Lipocalyx includes the following contingent cash considerations to the previous owners:

At the acquisition date, the fair value of the contingent consideration was k€572. The contingent consideration is presented in ‘non-current financial liabilities’ in the interim condensed consolidated statements of financial position.

The Group calculates the interim income tax expense using the tax rate that would be applicable to the expected total annual earnings. Deferred tax assets on tax losses of subsidiaries incorporated in Germany have not been capitalized as there is not sufficient probability that there will be future taxable profits against which the unused tax losses can be utilized. Deferred tax assets calculated from tax losses of subsidiaries incorporated in the United States incurred since the acquisition of BioNTech US have been recorded in an amount of k€2,317. Deferred tax assets have been offset with deferred tax liabilities recognized as part of the acquisition of BioNTech US (see Note 5) given that the conditions to offset were fulfilled. Accumulated tax losses relate to Germany and the United States. There is no expiration date for any of the accumulated tax losses under German tax law. With respect to accumulated losses incurred at the level of BioNTech USA Holding LLC and BioNTech Research and Development Inc. since their incorporation and tax losses of BioNTech US since the acquisition of BioNTech US there is no expiration date under U.S. tax law.

During the six months ended June 30, 2020, the Group acquired intangible assets with a cost of k€4,175 (six months ended June 30, 2019: k€10,451), excluding intangible assets acquired through business combinations (see Note 5). The acquisitions during the six months ended June 30, 2020 mainly related to advance payments (k€2,957) as well as concessions, licenses, in-process R&D and similar rights (k€1,218). During the six months ended June 30, 2019, the acquisitions mainly related to concessions, licenses, in-process R&D and similar rights (k€7,029) as well as to advance payments (k€3,422).

During the six months ended June 30, 2020, the Group acquired property, plant and equipment with a cost of k€21,396 (six months ended June 30, 2019: k€10,609), excluding property, plant and equipment acquired through business combinations (see Note 5). The acquisitions during the six months ended June 30, 2020 were related to construction in progress and advance payments (k€14,780), equipment, tools and installations (k€4,201) as well as land and buildings (k€2,415). During the six months ended

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June 30, 2019, the acquisitions were related to equipment, tools and installations (k€5,743), construction in progress and advance payments (k€4,224) as well as land and buildings (k€642).

Set out below, is an overview of financial assets, other than cash and cash equivalents, held by the Group as of June 30, 2020 and December 31, 2019:

Financial assets at amortized cost

Set out below, is an overview of financial liabilities held by the Group as of June 30, 2020 and December 31, 2019:

Financial liabilities at amortized cost (including interest-bearing loans and borrowings)