Spread a kitchen towel on the counter. Use your jar lifter to remove a warm jar from the canner. Empty the water and place it on the towel. Keep the remaining jars in the canner so they stay warm.
Place the canning funnel on the jar. Use a slotted spoon or tongs to remove the beets from the brine and fill the jar. Leave 1/2-inch headspace at the top of the jar.
Run the bubble popper through the jars to release air bubbles and wipe the rims. Adjust the headspace again if needed.
Center a lid on the jar, and screw on the band until it is fingertip tight. Use the jar lifter to place the jar back into the canner and repeat with the remaining jars.
Once all the jars are in the canner, adjust the water level so it is 2 inches above the tops of the jars.
Cover the canner and bring to boil over high heat. Once the water boils vigorously, continue boiling and process half-pints and pints for 30 minutes at altitudes less than 1,000 feet. Adjust processing time for your altitude if necessary (See Note).
When the processing time is complete, turn off the heat, remove the cover, and allow the canner to cool down and settle for about 5 minutes.
Spread a dry kitchen towel on the counter. Use the jar lifter to remove the jars from the canner and place them on the towel. Keep the jars upright, and don't tighten bands or check the seals yet. Let the jars sit undisturbed for 12 to 24 hours to cool.
After 12 to 24 hours, check to be sure jar lids have sealed by pushing on the center of the cover. The top should not pop up. If the lid flexes up and down, it did not seal. Refrigerate the jar and use it up within a week.
Remove the screw-on bands, rinse the jars, label, date, and store in a cool, dark location. Allow 4 weeks for the pickled beets to develop flavor. Use home canned jars within 12 to 18 months for the best quality. Makes about 6 pints or 12 half-pint jars.