Sechium compositum (Cucurbitaceae) is a wild species that is distributed in the Soconusco region, Chiapas, Mexico, and the border with Guatemala. This species has an intangible biochemical value resulting from the pharmacological relevance of its secondary metabolites. However, as a consequence of the lack of knowledge about its importance, it is being displaced from its habitat at an accelerated rate, incurring the risk of genetic loss. Therefore, an in vitro culture protocol with two experimental phases was evaluated to propagate, conserve, and regenerate this species. The first phases considered the shoot propagation, adding seven concentrations (0.1, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2 mg mL−1) of 6-benzylaminopurine (BA) and thidiazuron (TDZ) and evaluating the number of buds and shoots and the shoot height. The best multiplication response was recorded with 0.1, 0.2, 0.4, and 1.0 mg L−1 of BA and 0.1 mg L−1 of TDZ, as well as the MS base culture medium. The validation of the results of the first phase (0.1 mg L−1 of BA) was compared with the MS in an independent experiment against the control (n = 50 repetitions), obtaining a height of 52 mm, 1.36 shoots, and 9.22 buds, suggesting that this concentration is adequate for the purpose, surpassing the MS control (MS culture medium alone). Of the total volume of roots obtained with packed bud structure in the previous experimental sample, it was reduced to 14% (n = 50). The second phase consisted of inducing callus formation from stem and leaf explants through the addition of 0.5, 1.0, and 2.0 mg L−1 of TDZ and 2,4-Dichlorophenoxyacetic acid (2,4-D) to the medium. Callus induction in S. compositum was better when using the stem in a medium with 2.0 mg L−1 of 2,4-D with a value of 97.8% around the explant. The addition of 500 mg L−1 of polyvinylpyrrolidone (PVP) is also suggested to reduce oxidation. This protocol represents a significant advance in the conservation, multiplication, and callus formation of S. compositum and contributes to its rescue and revaluation in the face of the danger of extinction.