This research explores the determination of partial safety factors for Persian historical masonry walls, following Eurocode-6 principles, which account for material and geometric uncertainties. The study explores the impact of lateral constraints or boundary conditions (B.C.), Height-Length Proportion (α), the thickness of wall (t), and pre-compression levels as a gravity loading (P) on the structural behavior of these walls when subjected to uncertain conditions. Nonlinear pushover analyses were carried out on 200 masonry wall specimens, considering four α, ten variations in B.C. (including the impact of vertical (lateral walls) and horizontal (upper slabs) components), and three standard t (0.20, 0.35, and 0.50 m), all subjected to three different P (0.05, 0.1, and 0.2 MPa). The research also evaluates how variations in the modulus of elasticity and t affect the results under nonlinear analysis. Findings show that the Maximum Shear Capacity (Fu), maximum drift limit (δu/H), and effective stiffness (𝐾𝑒ff) are highly responsive to these variables. Higher Fu and 𝐾𝑒ff were observed with increased t, P, and B.C., while reducing α had the opposite effect. As B.C., t, and P increased, δu/H showed a reduction, while a decrease in α led to an increase. The estimated Fu ranged 114.8–1476.5 kN, δu/H varied 1.56–3.43, and 𝐾eff spanned 7.72–250.80 kN/mm. The proposed partial safety factors are 1.17–1.96 for material strength (γM), 1.16–1.77 for displacement capacity (γdu), and 1.15–1.96 for effective stiffness (γk). The results emphasize that increasing B.C., t, and reducing α result in higher γM and γk values, while γdu values decrease. Additionally, all safety factors rise with increased P. These findings offer important insights for enhancing the preservation of Persian historical masonry structures.