This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for sheep and goats stunned with the head-only electrical method or slaughtered without stunning. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. In the case of slaughter with head-only electrical stunning, the opinion proposes a toolbox to assess consciousness at three key stages of monitoring: (a) after electrical stunning and during shackling and hoisting, (b) during neck cutting and (c) during bleeding. For slaughter without stunning, another toolbox is proposed for (a) assessing unconsciousness before releasing the animals from restraint, and (b) confirming death before carcass dressing begins. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about the sensitivity, specificity and feasibility of the indicators. On the basis of such information, a methodology was developed to select the most appropriate indicators to be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring animal welfare. The personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning or before releasing from the restraint. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals to be checked at a given throughput rate (total number of animals slaughtered in the slaughterhouses) and threshold failure rate (number of potential failures—proportion of animals that are conscious after stunning). Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.