We study deviations between MSSM and NMSSM in the predictions of $\Delta F=2$ processes. We found that there can be two sources which can cause such deviations, i.e due to certain neutralino-gluino crossed box diagrams and due to well known double penguin diagrams. Both are effective at large $\tan \beta$. In addition to this, taking into account 8 TeV direct search constraints from the heavy Higgs searches, we study the maximum allowed MFV like new physics(NP) effects on $\Delta M_s$ in the two models. In NMSSM such NP effects can be as large as $25 \%$, on the other hand in MSSM such large contributions are severely constrained.