Hi SreejithN,
I didn't see clock configuration changed in startup code:

Note FOPT[LPBOOT] controls the reset value of clock divider of IRC 48 Mhz to feed the Core and platform clocks.
![FTFC_FOPT[LPBOOT].png FTFC_FOPT[LPBOOT].png](https://community.nxp.com/t5/image/serverpage/image-id/217961iA7795ADC8D129E78/image-size/large?v=v2&px=999)
Here is the Default configuration after reset:


I think you can refer to the S32K1 SDK example to initialize the clock module in the main function:
/* Initialize clock module */
status = CLOCK_DRV_Init(&clockMan1_InitConfig0);
Best Regards,
Robin
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