In recent years, nickel (Ni) deficiency symptoms has been observed in commercial pecan [Carya illinoinensis (Wangenh.) K. Koch.] orchards in New Mexico. Nickel deficiency can cause a reduction in lignin formation, which could affect the risk for breakage on pecan tree shoots. Ni deficiency might furthermore disrupt ureide catabolism in pecan and, therefore, could negatively affect nitrogen (N) nutrition in the plant. The objective of this study was to identify the effects of Ni and N fertilizer applications, at two rates, on net photosynthesis (Pn), leaf greenness (SPAD), and branch lignin concentration in New Mexico’s nonbearing pecan trees. Sixty trees for year 2012 (Pawnee and Western cultivars) and 40 trees for year 2013 (Pawnee cultivar) were used at two New Mexico locations (Artesia and Las Cruces) to evaluate the effects of Ni and N on tree measures. Treatments were as follows: (1) High N plus Ni (+Ni); (2) Low N no Ni (−Ni); (3) High N −Ni; and (4) Low N +Ni. In 2012 and 2013, there was an increase in leaf greenness for each location and cultivar (tree group) through time (June to September). Photosynthesis measures in 2012 differed between tree group, time in the season, and N and Ni treatments. In 2013, Pn was influenced by tree group and time (P < 0.0001), but N and Ni interaction did not present a significant effect related to Ni benefits. Photosynthesis varied over time in 2012 and 2013, with an inconsistent pattern. In this study, Ni application at the high N rate had a negative effect on ‘Pawnee’ Pn early in the season at the Artesia site, but this application had a positive effect for ‘Western’ from Artesia at the low N level, also early in the season. Lignin content varied between tree groups only. The application of N and Ni did not affect lignin in pecan shoots. The results show an inconsistent pattern regarding the benefits of Ni on nonbearing pecan orchards for leaf greenness, Pn, and lignin content during the 2-year study. Future studies on Ni should focus on pecan trees exhibiting leaf Ni deficiency symptoms or on soils with less than 0.14 mg·kg−1 of DTPA extractable Ni, as well as the long-term effect of Ni on pecan growth and development to optimize the addition of Ni into an efficient fertilization program.