<p class="Newparagraph"><strong>Background: </strong>The sexual propagation of Cocoa (<em>Theobroma cacao</em> L.) has some limitations to preserve some desirable agronomic characteristics in successive generations.<strong> Objective:</strong> The present research evaluates the effect of a chitosan based-formulation (Quitomax®) on morpho-physiological, rooting attributes and benefit-cost ratio of two cocoa varieties during vegetative propagation. <strong>Methodology:</strong> The experimental design was completely randomized with a factorial arrangement (A × B), where A represented the two clones and B the three concentrations of chitosan based formulation used (0, 100, 500 and 1000 mg L<sup>-1</sup>), with three repetitions. per treatment. The survival (%), the stem diameter (mm), the number of leaves, the number and length (cm) of roots, the biomass (g), the gas exchange (A, gs, Ci, E), and an economic analysis of the two cocoa plant varieties were evaluated at 120 days after starting the trial. <strong>Results:</strong> The clone CCN-51 treated with 500 mg L<sup>-1</sup> had significantly the highest results on survival (80%), stem diameter (6.83 mm), number of leaves per plant (8.2), number and length of roots (6.21 and 35.74 cm), aerial and root biomass (4.07 g and 1.64 g) parameters. In gas exchange, the highest values of Water use efficiency (WUE) were observed at 500 mg L<sup>-1</sup> in CCN-51 (5.36 mmol mol<sup>-1</sup>) and 1000 mg L<sup>-1</sup> in INIAP-EETP-801 (7.62 mmol µmol<sup>-1</sup>). In both clones, higher profitability was obtained when applying the chitosan dose of 500 mg L<sup>-1</sup>, reaching profitability of 40.65 and 50.00% for clones INIAP-EETP-801 and CCN-51, respectively. <strong>Implications:</strong> The cocoa clone CCN-51 showed plants that exhibited greater development of both the aerial part and the root part of the cocoa seedlings than INIP-EETP-801 coca clones. <strong>Conclusion:</strong> The chitosan based formulation at 500 mg L<sup>-1</sup> is a promissory alternative to improve the evaluated parameters after 120 days of cocoa vegetative propagation.</p>