Despite common assertions that puppies acquired from low-welfare sources (e.g. ‘puppy farms’) and/or sold illegally (e.g. without buyers seeing their puppies’ mother pre-purchase) have poorer future health and welfare, remarkably little evidence supports this. We investigated the impact of puppy early-life risk factors, including owner acquisition behaviours, upon adult dog health outcomes. An online longitudinal survey followed a cohort of n = 985 ‘Pandemic Puppies’ purchased in the UK during 2020 aged < 16 weeks of age as they reached 21 months of age. Owners reported their dogs’ diagnosed health disorders and their expectations vs realities of veterinary costs since a ‘puppyhood’ questionnaire (while ≤ 7 months of age) in 2020. Multivariable modelling investigated risk factors for these outcomes, including early-life health, behaviour, and acquisition-related variables. Most owners (n = 931/985; 94.5%) reported ≥ one health problem in their dog since the 2020 questionnaire. Puppies sold < 6 weeks of age, without their owner having seen the puppy’s mother prior to purchase, or acquired by first-time owners were more likely to have a higher number of health disorders at 21 months old. One-quarter (n = 220/936; 23.5%) of owners had spent more than they expected on veterinary costs since acquiring their puppy, with owners of puppies sold without a microchip more likely to report this. Results suggest that longer-term health outcomes are linked to how and where a puppy is acquired. As many risk factors identified here are already illegal in England, Wales and Scotland, greater enforcement and awareness of this legislation is urgently needed to protect canine welfare.