Capsicum annuum varieties are highly sensitive to drought. Under water stress conditions, these can show yield losses of up to 70 %. Due to the above, this work proposes a novel approach to obtain estimators of drought stress based on linear regression models for morpho-physiological and biochemical variables in jalapeño pepper (C. annuum cv. jalapeno M), bell pepper (C. annuum cv. california wonder), and serrano pepper (C. annnuum cv. serrano tampiqueno). Jalapeno pepper plants were grown for 69 days under permanent water deficit conditions at 40, 60, 80 % and 100 % of field capacity (FC) (100 % FC as control). Throughout the crop cycle, we monitored the plant's height and weight, basal stem diameter, transpiration, photosynthesis, stomatal conductance, NDVI, and proline. This monitoring allowed us to obtain linear regression models from the accumulated values for these variables, from which the slope values (β) were used as estimators of drought stress using the interval estimation method, in the same way, this method was used to estimate water status in bell pepper and serrano pepper. For bell pepper, drought levels of 40, 60, 80 and 100 % FC were imposed for 12 days and serrano pepper 60 and 100 % FC for 63 days. The results showed that this method can be used to estimate drought stress in jalapeno pepper for all the irrigation levels through photosynthesis and NDVI and can be applied for bell pepper and serrano pepper using stem diameter and plant height, and in the case of serrano pepper, NDVI showed adequate results. Also, this work establishes the relationship between the jalapeno pepper responses (morpho-physiological and biochemical) to drought stress during vegetative, flowering, and fruiting stages through a Principal Component Analysis (PCA). The PCA found that interaction among morphological, physiological, and biochemical responses change concerning the phenological stage of the plant. The results suggested several direct and inverse relationships between the variables and showed that drought can be described by stomatal conductance during any phenological stage of the crop. In parallel, the proline content, NDVI and plant height can also describe drought stress during the vegetative and flowering stages. This research is the first to apply this methodology to drought stress estimation in jalapeno, bell pepper, and serrano pepper cultivation. The results could significantly contribute to precision agriculture, sensor development, and water management.