This study endeavors to ascertain alterations in the in-line registered milk fat-to-protein ratio as a potential indicator for evaluating the metabolic status of dairy cows. Over the study period, farm visits occurred biweekly on consistent days, during which milk composition (specifically fat and protein) was measured using a BROLIS HerdLine in-line milk analyzer (Brolis Sensor Technology, Vilnius, Lithuania). Clinical examinations were performed at the same time as the farm visits. Blood was drawn into anticoagulant-free evacuated tubes to measure the activities of GGT and AST and albumin concentrations. NEFA levels were assessed using a wet chemistry analyzer. Using the MediSense and FreeStyle Optium H systems, blood samples from the ear were used to measure the levels of BHBA and glucose in plasma. Daily blood samples were collected for BHBA concentration assessment. All samples were procured during the clinical evaluations. The cows were categorized into distinct groups: subclinical ketosis (SCK; n = 62), exhibiting elevated milk F/P ratios without concurrent clinical signs of other post-calving diseases; subclinical acidosis (SCA; n = 14), characterized by low F/P ratios (<1.2), severe diarrhea, and nondigestive food remnants in feces, while being free of other post-calving ailments; and a healthy group (H; n = 20), comprising cows with no clinical indications of illness and an average milk F/P ratio of 1.2. The milk fat-to-protein ratios were notably higher in SCK cows, averaging 1.66 (±0.29; p < 0.01), compared to SCA cows (0.93 ± 0.1; p < 0.01) and healthy cows (1.22). A 36% increase in milk fat-to-protein ratio was observed in SCK cows, while SCA cows displayed a 23.77% decrease. Significant differences emerged in AST activity, with SCA cows presenting a 26.66% elevation (p < 0.05) compared to healthy cows. Moreover, SCK cows exhibited a 40.38% higher NEFA concentration (p < 0.001). A positive correlation was identified between blood BHBA and NEFA levels (r = 0.321, p < 0.01), as well as a negative association between BHBA and glucose concentrations (r = −0.330, p < 0.01). Notably, AST displayed a robust positive correlation with GGT (r = 0.623, p < 0.01). In light of these findings, this study posits that milk fat-to-protein ratio comparisons could serve as a non-invasive indicator of metabolic health in cows. The connections between milk characteristics and blood biochemical markers of lipolysis and ketogenesis suggest that these markers can be used to check the metabolic status of dairy cows on a regular basis.