The Health Services Provision Assessment in Ethiopia (SPA-ET) is a survey that generates data on the availability and quality of health services in Ethiopia. Despite the presence of integrated management of childhood illness guidelines in healthcare settings, there has been inadequate exploration or assessment of how effectively and consistently health professionals follow the guidelines. This study aims to identify factors influencing healthcare worker adherence to the integrated management of childhood illness guidelines to identify spatial clusters. The data for this study were gathered from the Service Provision Assessment (SPA) survey in Ethiopia, which was conducted nationwide from August 11, 2021, to February 4, 2022. It included a total of 788 health professionals who assessed sick children experiencing at least one of the three main childhood illness symptoms: fever, cough, or diarrhea. We employed STATA version 16 for data analysis, utilizing cross-tabulations to explore relationships between variables and logistic regression modeling to identify factors influencing adherence. To account for the hierarchical structure of the health survey data, we employed multilevel logistic regression. Model selection was based on comparison parameters including the Bayesian Information Criterion (BIC) and Akaike Information Criterion (AIC). We computed adjusted odds ratios with 95% confidence intervals, and statistical significance was determined at a significance level of p < 0.05. The rate of adherence to the integrated management of childhood illness guideline was 33% (95% CI: 29.70%, 36.26%). The analysis revealed several factors influencing adherence to IMCI protocols. child's age (being ≥24 months) [aOR = 0.66, 95% CI: (0.45, 0.87)], facility type (health center) [aOR = 2.61, 95% CI: (1.84, 3.37)], place of residency (being rural) [aOR = 0.54, 95% CI: (0.38, 0.77)], and care provider's qualification (health officer) [aOR = 1.71, 95% CI: (1.18, 2.48)] were all statistically significant. Moreover, the primary cluster is situated in the west Oromia region, with a central focus at coordinates (7.982108 N, 36.203355 E) and extends to a radius of 78.28 km. This study confirms a low adherence rate (33%) among health professionals in Ethiopia to the IMCI guideline for assessing the three main symptoms of sick children. The study identified child's age, facility type, academic qualification, and place of residence as crucial factors correlated with adherence rate. Furthermore, 5 secondary clusters (hotspot areas) were identified using SaTScan software. To address the higher protocol refusal, interventional plan needs to be based on academic qualification of care provider, facility type, age of child and place of residency. Moreover, interventions to reduce non-adherence to IMCI guidelines should be location-tailored based on identified hotspot areas to restore guidelines adherence equality.