In developing countries, intercropping is commonly used to boost land productivity and agricultural benefits. However, in the Yucatan region of Mexico, maize (Zea mays L.) yields remain low, despite consistent fertilizer and pesticide inputs in traditional intercropping systems. Furthermore, little is known about the photosynthetic mechanisms that occur when maize plants interact with legumes, and there is a lack of understanding of how intercropping systems affect other organisms in the system, such as beneficial and insect pest population dynamics. A field experiment was carried out on the Yucatan Peninsula in 2021 to assess the impact of maize–legume intercropping systems on maize yield, physiological characteristics as evaluated by gas exchange measurements, and the abundance of beneficial insects in traditional and novel maize intercropping systems. The experiment was carried out with a randomized complete block design with three replicates. Treatments included maize intercropped with a novel legume, crotalaria (Crotalaria juncea L.), maize intercropped with a traditional legume, cowpea (Vigna unguiculata (L.) Walp.), and sole maize as a control. Significant differences in plant height were shown at growth stages V12 (45 days after sowing) and VT (60 days after sowing). No differences were observed in stem diameter, leaf area index, or chlorophyll content. The maize/cowpea intercrop increased the photosynthesis rate by 12.9% and 9.84% in the maize/crotalaria and sole maize, respectively (p < 0.001), and transpiration rate by 6.5% and 8.5% in the maize intercropped with crotalaria and sole maize treatments, respectively (p < 0.001), of maize plants. No significant effects on stomatal conductance or water use efficiency were observed, but the carbon intercellular rate was reduced by 9.74% and 9.15 when compared to the maize/crotalaria and the sole maize treatments, respectively. Overall, intercropping treatments attracted more beneficial insects than sole maize. For predators, the families that stood out were Coccinelidae, Formicidae, Araneidae, Thomisidae, Syrphidae, Chrysomelidae, Oxypidae, Vespidae, Reduviidae, Carabidae, Asilidae, Salthicidae, Dolichopodidae, while among parasitoids, the most frequent families were Eurytomydae, Braconidae, Tachinidae, Pteromalidae, Scelionidae, and Figitidae. In comparison to the maize/cowpea and maize/crotalaria treatments, the sole maize treatment resulted in a grain yield increase of 24.5% and 32%, respectively. However, sole maize was not statistically different to that of maize/cowpea intercropping. In conclusion, our findings suggest that maize/cowpea intercropping could be a viable alternative to sole maize cropping systems for enhancing maize yield and the abundance of beneficial insects, without increasing interspecific competition with the maize crop. Therefore, the maize/cowpea intercropping system represents a sustainable planting alternative for promoting maize grain yield and also promoting edible legume production within the system. Furthermore, the outcomes of this study can serve as a theoretical framework for increasing maize–legume intercropping profitability under growing conditions on the Yucatan Peninsula.