Palmitoleic acid (C16:1) is rare among woody oil crops yet accumulates to high levels in macadamia kernels, where its inter-accession variation and relationship with fruit traits remain poorly characterized. We profiled 22 fatty acids by GC-MS, quantified crude fat, crude protein and total soluble sugar by NIRS, and measured nine fruit traits in 139 accessions. The major fatty acids ranked as C18:1 > C16:1 > C16:0. C16:1 varied widely among accessions (mean 10.66%, CV = 27.7%, range 2.78–19.05%), about 12-fold the analytical RSD, whereas C18:1 was stable (CV = 5.3%). C16:1 was strongly negatively correlated with C18:1 (r = −0.921, p < 0.001) and positively correlated with C16:0 (r = 0.534). Correlation, partial correlation and PCA consistently indicated that fatty acid composition was independent of fruit traits; after controlling for C18:1, C16:1 retained only a weak positive association with single dry kernel weight (r = 0.170, p < 0.05). Entropy-weighted TOPSIS with five indicators selected five accessions combining high C16:1 with desirable fruit traits. These accessions provide breeding material for C16:1-enriched oil, and the independence of C16:1 from fruit traits means that both can be improved simultaneously.