The Court held that, when a farmer plants a harvested and saved seed, thereby growing another soybean crop, that action constitutes an unauthorized "making" of the patented product.

[3] Commentators noted, however, that the Court's ruling was narrow in scope, and did not set a broad legal precedent with respect to the applicability of the doctrine of patent exhaustion to self-replicating technologies.

[7] He replanted seeds from the original second harvest in subsequent years for his second seasonal planting, supplementing them with more soybeans he bought at the elevator.

[6] The court held that since the original farmers could not use the later generation seeds without a license, they could not make an unrestricted sale and therefore the patent rights were not exhausted.

[6] Bowman argued that the Monsanto license agreement allowed the sale of second-generation soybeans to both grain elevators and subsequent buyers and that this caused the patent rights to be exhausted per the United States Supreme Court's ruling in Quanta Computer, Inc. v. LG Electronics, Inc.[6][12] Monsanto argued that the license agreement specifically prohibited the use of second-generation seeds for planting.

[6] Bowman argued that the Federal Circuit's decision conflicted with existing Supreme Court precedent on patent exhaustion.

[6] He claimed that the Federal Circuit had created a judicial exception to patent exhaustion for Monsanto, allowing it to dominate the soybean seed market.

[6] Monsanto argued that the second-generation seeds were not subject to exhaustion because they had not existed until Bowman created them and had not been sold at the time of infringement.

Because Justice Clarence Thomas had served as a lawyer for the Monsanto Company 34 years earlier, some critics questioned whether he would remain impartial.

[19] However, Mann also predicted that "it seems most unlikely the Court will rule against Monsanto",[18] and in his coverage of the case's oral arguments, he observed that "none of the Justices expressed any sympathy for [Bowman’s] position".

An academic co-author of an amicus brief on behalf of Bowman filed by the American Antitrust Institute expressed relief that the loss was on a narrow basis rather than providing a broad affirmation of the lack of patent exhaustion for self-replicating technologies.

[22] Kevin Rodkey argued that an analysis under Quanta Computer leads to the conclusion that patent rights covering self-replicating seeds are exhausted on the first authorized sale, including subsequent generations, and that seed companies can only exclude subsequent replantings with carefully written license restrictions.

[25] Rochelle C. Dreyfus is also reported to have criticized the decision, noting that Bowman was attempting to obtain the benefit of the genetic modifications, while others, such as organic growers, fear being sued for inadvertent cross-contamination.

[26] Additionally, the Harvard Law Review wrote that "[t]he Court reached the correct outcome but via the wrong route" because its ruling "obfuscates the role of the licensing agreement" and because the "exhaustion doctrine is ill suited to address the challenges posed by self-replicating technologies".

Tabetha Marie Peavey suggested that the Court "appeared to be alert to the consequences of its ruling, not just for the value of Monsanto’s soybean patents, but also for technologies like cell lines, software, and vaccines".