Appraising employee performance from the perspective of Internal Business Process (IBP) perspective is a dimension of performance appraisal exercise that is not only misunderstood but neglected or given little or no attention. Evaluating performance based on IBP benchmarks and established milestones using the Staff Performance Appraisal and Development (SPADEV) reporting system in the Civil Service of Lagos State, Nigeria is counter-productive. Lack of unambiguous rules and unwritten codes of conduct in basic organizational operating environments give rise to vague performance appraisal mechanisms, processes and outcomes. These reasons contributed to the inadequacies of the Annual Performance Evaluation and Reporting (APER) system previously used in the Civil Service of Lagos State, Nigeria and also constitutes a threat to the effectiveness of the Staff Performance Appraisal and Development (SPADEV) Reporting System. This comparative study examined the Effect of Internal Business Process (IBP) perspective on Performance Appraisal using The Balanced Scorecard of Objective (BSCO) Method or The Staff Performance Appraisal and Development (SPADEV) Reporting Method in the Civil Service of Lagos State, Nigeria. Descriptive survey design was adopted for this study with Key Informant Interviews (KII). The population comprised fourteen Ministries, the Civil Service Commission (CSC), and the Office of Transformation, Creativity and Innovation (OTCI) with total staff strength of 7,555 in the Lagos State Civil Service. Utilizing Taro Yamane’s sampling technique, a sample size of 380 participants was arrived at, with a thirty percent (30%) addition (to enhance the confidence level and response rate). A self-developed structured questionnaire was used to collect information about variables that formed the basis for assessing the appraisal instruments, BSCO and SPADEV; from the perspective of the level of appropriateness (App). The questionnaire was validated, yielding a Cronbach’s alpha coefficient of 0.830. A total of 494 copies of the questionnaire documents were distributed, with a response rate of about 75%. In addition, two Commissioners and a Director General were interviewed, using interview-guide. Data from the questionnaire were analyzed using descriptive and inferential analyses (p=0.05) while data from the interview were content- analyzed. Findings revealed that there was significant difference (p<0.003) between BSCO (IBP: = 7.20) and SPADEV (IBP: = 2.84) for criterion variables assessing the appraisal instruments. Furthermore, analysis of KII revealed BSCO appraisal method to be superior to SPADEV method of appraisal. The study concluded that evaluating employee performance from the Internal Business Process perspective (IBP) using the BSCO is more viable than SPADEV with consistently significant difference for all variables used in assessing the appraisal instruments. It is therefore clear from the study that there is a significantly positive effect of the Internal Business Process (IBP) perspective in BSCO as an alternative to SPADEV. It therefore recommended that the IBPP should be used in BSCO as an alternative performance appraisal instrument in the Lagos State Civil Service.