But the centres, all members of the GCA network are still showing average overall year to date growth of 6.4%.
Clothing was up 16.71%, furniture and barbecues up 12.07% and houseplants up 7.31%.
Sales in catering were up 4.01% and food hall and farm shop up 0.8%. Hard landscaping sales were down -1.6%, gifts were down -1.93% and pets and aquatics sales were up 3.24%.
Garden sundries were up 0.2%, seeds and bulbs were down 12.91% and outdoor plants were down 3.18%.
GCA chief executive Iain Wylie said: "While clothing sales are not as high this month as they were for May, it was still the fastest growing category in our member garden centres for the month of June.
"The Great British weather was as unpredictable as ever during June, with the north receiving rain and the south remaining relatively warm and dry. We even experienced some rather hot weather for a brief period. The ever changing weather can cause uncertainty when it comes to gardening, which is why it seems customers stuck to buying in non-traditional categories, such as clothing."
Claire Salt, clothing and gift supervisor at Fairways Garden Centre, said: "For this season in particular we have focused on a more casual style of summer clothing and footwear in our clothing department. Our most popular lines without question have been the floaty Italian style of LV Clothing and the stylish yet reasonably priced shoes from our large offering from LJ&R Footwear."